data_1WJE

_pdbx_vrpt_database.id    PDB
_pdbx_vrpt_database.code  1WJE
#
_pdbx_vrpt_exptl.ordinal  1
_pdbx_vrpt_exptl.method   nmr
#
_pdbx_vrpt_summary.entry_id                    1WJE
_pdbx_vrpt_summary.PDB_deposition_date         1998-06-11
_pdbx_vrpt_summary.PDB_revision_number         5
_pdbx_vrpt_summary.PDB_revision_date           2024-05-01
_pdbx_vrpt_summary.report_creation_date        2024-04-20:21:52
_pdbx_vrpt_summary.attempted_validation_steps  mogul,molprobity,validation-pack,coreclust,chemicalshiftanalysis,percentiles,writepdf,writexml,writecif
_pdbx_vrpt_summary.ligands_for_buster_report   N
#
loop_
_pdbx_vrpt_entity.id
_pdbx_vrpt_entity.type
_pdbx_vrpt_entity.description
1  polymer      "HIV-1 INTEGRASE"  
2  non-polymer  "CADMIUM ION"  
#
loop_
_pdbx_vrpt_asym.label_asym_id
_pdbx_vrpt_asym.entity_id
A  1  
B  1  
C  2  
D  2  
#
loop_
_pdbx_vrpt_percentile_list.id
_pdbx_vrpt_percentile_list.range
_pdbx_vrpt_percentile_list.exp_method
1  all  pdb    
2  nmr  x-ray  
#
loop_
_pdbx_vrpt_percentile_type.id
_pdbx_vrpt_percentile_type.type
1  all_atom_clashscore           
2  Ramachandran_outlier_percent  
3  rotamer_outliers_percent      
#
loop_
_pdbx_vrpt_percentile_conditions.id
_pdbx_vrpt_percentile_conditions.percentile_list_id
_pdbx_vrpt_percentile_conditions.type_id
_pdbx_vrpt_percentile_conditions.rank
_pdbx_vrpt_percentile_conditions.number_entries_total
_pdbx_vrpt_percentile_conditions.res_high
_pdbx_vrpt_percentile_conditions.res_low
1  1  1   30.60  158937  ?     ?     
2  2  1   54.45   12864  ?     ?     
3  1  2  100.00  154571  ?     ?     
4  2  2  100.00   11451  ?     ?     
5  1  3    9.09  154315  ?     ?     
6  2  3   52.80   11428  ?     ?     
#
loop_
_pdbx_vrpt_percentile_entity_view.ordinal
_pdbx_vrpt_percentile_entity_view.conditions_id
_pdbx_vrpt_percentile_entity_view.type_id
_pdbx_vrpt_percentile_entity_view.label_asym_id
_pdbx_vrpt_percentile_entity_view.PDB_model_num
_pdbx_vrpt_percentile_entity_view.entity_id
_pdbx_vrpt_percentile_entity_view.auth_asym_id
_pdbx_vrpt_percentile_entity_view.rank
1  3  2  A  1  1  A  100.00  
2  4  2  A  1  1  A  100.00  
3  5  3  A  1  1  A    4.30  
4  6  3  A  1  1  A    4.30  
5  3  2  B  1  1  B  100.00  
6  4  2  B  1  1  B  100.00  
7  5  3  B  1  1  B    7.33  
8  6  3  B  1  1  B    7.33  
#
loop_
_pdbx_vrpt_summary_entity_geometry.ordinal
_pdbx_vrpt_summary_entity_geometry.PDB_model_num
_pdbx_vrpt_summary_entity_geometry.entity_id
_pdbx_vrpt_summary_entity_geometry.label_asym_id
_pdbx_vrpt_summary_entity_geometry.auth_asym_id
_pdbx_vrpt_summary_entity_geometry.angles_RMSZ
_pdbx_vrpt_summary_entity_geometry.bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_bonds_RMSZ
_pdbx_vrpt_summary_entity_geometry.num_angles_RMSZ
1  1  1  A  A  0.87  1.12  371  499  
2  1  1  B  B  0.87  1.12  371  499  
#
_pdbx_vrpt_summary_geometry.ordinal                                    1
_pdbx_vrpt_summary_geometry.percent_ramachandran_outliers_full_length  0.00
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers                   11.25
_pdbx_vrpt_summary_geometry.percent_rotamer_outliers_full_length       11.25
_pdbx_vrpt_summary_geometry.clashscore                                 9.76
_pdbx_vrpt_summary_geometry.clashscore_full_length                     9.76
_pdbx_vrpt_summary_geometry.num_H_reduce                               704
_pdbx_vrpt_summary_geometry.num_bonds_RMSZ                             742
_pdbx_vrpt_summary_geometry.bonds_RMSZ                                 1.12
_pdbx_vrpt_summary_geometry.num_angles_RMSZ                            998
_pdbx_vrpt_summary_geometry.angles_RMSZ                                0.87
#
loop_
_pdbx_vrpt_model_instance.id
_pdbx_vrpt_model_instance.PDB_model_num
_pdbx_vrpt_model_instance.entity_id
_pdbx_vrpt_model_instance.label_asym_id
_pdbx_vrpt_model_instance.label_seq_id
_pdbx_vrpt_model_instance.label_comp_id
_pdbx_vrpt_model_instance.auth_asym_id
_pdbx_vrpt_model_instance.auth_seq_id
_pdbx_vrpt_model_instance.label_alt_id
_pdbx_vrpt_model_instance.PDB_ins_code
_pdbx_vrpt_model_instance.count_clashes
 1  1  1  A   1  PHE  A   1  .  ?        ?  
 2  1  1  A   2  LEU  A   2  .  ?        ?  
 3  1  1  A   3  ASP  A   3  .  ?        2  
 4  1  1  A   4  GLY  A   4  .  ?        ?  
 5  1  1  A   5  ILE  A   5  .  ?        2  
 6  1  1  A   6  ASP  A   6  .  ?        ?  
 7  1  1  A   7  LYS  A   7  .  ?        ?  
 8  1  1  A   8  ALA  A   8  .  ?        ?  
 9  1  1  A   9  GLN  A   9  .  ?        ?  
10  1  1  A  10  GLU  A  10  .  ?        ?  
11  1  1  A  11  GLU  A  11  .  ?        ?  
12  1  1  A  12  CYS  A  12  .  ?        ?  
13  1  1  A  13  GLU  A  13  .  ?        2  
14  1  1  A  14  LYS  A  14  .  ?        ?  
15  1  1  A  15  TYR  A  15  .  ?        ?  
16  1  1  A  16  HIS  A  16  .  ?        4  
17  1  1  A  17  SER  A  17  .  ?        ?  
18  1  1  A  18  ASN  A  18  .  ?        ?  
19  1  1  A  19  TRP  A  19  .  ?        ?  
20  1  1  A  20  ARG  A  20  .  ?        ?  
21  1  1  A  21  ALA  A  21  .  ?        ?  
22  1  1  A  22  MET  A  22  .  ?        ?  
23  1  1  A  23  ALA  A  23  .  ?        1  
24  1  1  A  24  SER  A  24  .  ?        ?  
25  1  1  A  25  ASP  A  25  .  ?        ?  
26  1  1  A  26  PHE  A  26  .  ?        ?  
27  1  1  A  27  ASN  A  27  .  ?        1  
28  1  1  A  28  LEU  A  28  .  ?        ?  
29  1  1  A  29  PRO  A  29  .  ?        ?  
30  1  1  A  30  PRO  A  30  .  ?        ?  
31  1  1  A  31  VAL  A  31  .  ?        ?  
32  1  1  A  32  VAL  A  32  .  ?        ?  
33  1  1  A  33  ALA  A  33  .  ?        ?  
34  1  1  A  34  LYS  A  34  .  ?        ?  
35  1  1  A  35  GLU  A  35  .  ?        ?  
36  1  1  A  36  ILE  A  36  .  ?        ?  
37  1  1  A  37  VAL  A  37  .  ?        ?  
38  1  1  A  38  ALA  A  38  .  ?        1  
39  1  1  A  39  SER  A  39  .  ?        ?  
40  1  1  A  40  CYS  A  40  .  ?        ?  
41  1  1  A  41  ASP  A  41  .  ?        ?  
42  1  1  A  42  LYS  A  42  .  ?        ?  
43  1  1  A  43  CYS  A  43  .  ?        ?  
44  1  1  A  44  GLN  A  44  .  ?        1  
45  1  1  A  45  LEU  A  45  .  ?        ?  
46  1  1  A  46  LYS  A  46  .  ?        ?  
47  1  1  B   1  PHE  B   1  .  ?        ?  
48  1  1  B   2  LEU  B   2  .  ?        ?  
49  1  1  B   3  ASP  B   3  .  ?        2  
50  1  1  B   4  GLY  B   4  .  ?        ?  
51  1  1  B   5  ILE  B   5  .  ?        2  
52  1  1  B   6  ASP  B   6  .  ?        ?  
53  1  1  B   7  LYS  B   7  .  ?        ?  
54  1  1  B   8  ALA  B   8  .  ?        ?  
55  1  1  B   9  GLN  B   9  .  ?        ?  
56  1  1  B  10  GLU  B  10  .  ?        ?  
57  1  1  B  11  GLU  B  11  .  ?        ?  
58  1  1  B  12  CYS  B  12  .  ?        ?  
59  1  1  B  13  GLU  B  13  .  ?        2  
60  1  1  B  14  LYS  B  14  .  ?        ?  
61  1  1  B  15  TYR  B  15  .  ?        ?  
62  1  1  B  16  HIS  B  16  .  ?        4  
63  1  1  B  17  SER  B  17  .  ?        ?  
64  1  1  B  18  ASN  B  18  .  ?        ?  
65  1  1  B  19  TRP  B  19  .  ?        ?  
66  1  1  B  20  ARG  B  20  .  ?        ?  
67  1  1  B  21  ALA  B  21  .  ?        ?  
68  1  1  B  22  MET  B  22  .  ?        ?  
69  1  1  B  23  ALA  B  23  .  ?        1  
70  1  1  B  24  SER  B  24  .  ?        ?  
71  1  1  B  25  ASP  B  25  .  ?        ?  
72  1  1  B  26  PHE  B  26  .  ?        ?  
73  1  1  B  27  ASN  B  27  .  ?        1  
74  1  1  B  28  LEU  B  28  .  ?        ?  
75  1  1  B  29  PRO  B  29  .  ?        ?  
76  1  1  B  30  PRO  B  30  .  ?        ?  
77  1  1  B  31  VAL  B  31  .  ?        ?  
78  1  1  B  32  VAL  B  32  .  ?        ?  
79  1  1  B  33  ALA  B  33  .  ?        ?  
80  1  1  B  34  LYS  B  34  .  ?        ?  
81  1  1  B  35  GLU  B  35  .  ?        ?  
82  1  1  B  36  ILE  B  36  .  ?        ?  
83  1  1  B  37  VAL  B  37  .  ?        ?  
84  1  1  B  38  ALA  B  38  .  ?        1  
85  1  1  B  39  SER  B  39  .  ?        ?  
86  1  1  B  40  CYS  B  40  .  ?        ?  
87  1  1  B  41  ASP  B  41  .  ?        ?  
88  1  1  B  42  LYS  B  42  .  ?        ?  
89  1  1  B  43  CYS  B  43  .  ?        ?  
90  1  1  B  44  GLN  B  44  .  ?        1  
91  1  1  B  45  LEU  B  45  .  ?        ?  
92  1  1  B  46  LYS  B  46  .  ?        ?  
93  1  2  C   .  CD   A  56  .  ?        ?  
94  1  2  D   .  CD   B  56  .  ?        ?  
#
loop_
_pdbx_vrpt_model_instance_geometry.ordinal
_pdbx_vrpt_model_instance_geometry.instance_id
_pdbx_vrpt_model_instance_geometry.rotamer_class
_pdbx_vrpt_model_instance_geometry.phi
_pdbx_vrpt_model_instance_geometry.psi
_pdbx_vrpt_model_instance_geometry.ramachandran_class
_pdbx_vrpt_model_instance_geometry.num_H_reduce
_pdbx_vrpt_model_instance_geometry.num_bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.bonds_RMSZ
_pdbx_vrpt_model_instance_geometry.num_angles_RMSZ
_pdbx_vrpt_model_instance_geometry.angles_RMSZ
_pdbx_vrpt_model_instance_geometry.program_for_bond_angle_geometry
 1   1  m-85          ?       ?  ?        11  12  1.35  16  0.77  molprobity  
 2   2  mt       -104.3   145.4  Favored  11   8  1.03  11  0.89  molprobity  
 3   3  m-20      -60.0   -39.2  Favored   4   8  0.97  11  0.82  molprobity  
 4   4  ?         -46.3   -15.6  Allowed   3   4  1.68   5  0.90  molprobity  
 5   5  mt        -60.1   -40.0  Favored  11   8  0.87  11  0.89  molprobity  
 6   6  OUTLIER   -59.3   -39.6  Favored   4   8  1.20  11  0.71  molprobity  
 7   7  tttm      -62.8   -40.0  Favored  13   9  0.89  11  0.92  molprobity  
 8   8  ?         -61.5   -35.5  Favored   5   5  1.02   7  0.64  molprobity  
 9   9  mt-30     -60.0   -40.0  Favored   8   9  0.94  12  0.83  molprobity  
10  10  tt0       -61.4   -40.0  Favored   6   9  1.63  12  0.82  molprobity  
11  11  mt-10     -95.9     6.6  Favored   6   9  1.64  12  0.91  molprobity  
12  12  t         -51.0   -41.9  Favored   4   6  0.90   8  1.05  molprobity  
13  13  mt-10     -60.0   -36.0  Favored   6   9  1.66  12  0.81  molprobity  
14  14  tttm      -64.9   -39.5  Favored  13   9  0.89  11  0.79  molprobity  
15  15  m-85      -85.5   -12.1  Favored   9  13  1.31  18  1.07  molprobity  
16  16  OUTLIER    57.7  -134.7  Allowed   7  11  0.81  15  0.62  molprobity  
17  17  OUTLIER   -84.7    -3.9  Favored   5   6  0.97   8  0.76  molprobity  
18  18  m-20      -80.3    76.5  Favored   6   8  0.97  11  0.82  molprobity  
19  19  p-90      -70.0   -26.6  Favored  10  16  1.07  23  1.51  molprobity  
20  20  mtt180    -60.0   -41.0  Favored  13  11  1.25  14  1.09  molprobity  
21  21  ?         -66.0   -42.0  Favored   5   5  0.96   7  0.59  molprobity  
22  22  ttp       -62.2   -44.6  Favored   9   8  0.86  10  1.03  molprobity  
23  23  ?         -57.5   -39.8  Favored   5   5  1.00   7  0.60  molprobity  
24  24  OUTLIER   -66.2   -38.0  Favored   5   6  1.02   8  0.71  molprobity  
25  25  m-20      -70.0   -41.9  Favored   4   8  1.12  11  0.63  molprobity  
26  26  m-85      -95.5    -0.2  Favored   9  12  1.36  16  0.75  molprobity  
27  27  m120       53.2    47.2  Favored   6   8  0.94  11  0.82  molprobity  
28  28  mt       -113.5   150.7  Favored  11   8  1.16  12  0.74  molprobity  
29  29  Cg_endo   -70.3   154.0  Favored   7   8  0.83  12  0.45  molprobity  
30  30  Cg_exo    -43.4   -23.4  Allowed   7   8  0.86  11  0.70  molprobity  
31  31  t         -60.0   -50.7  Favored   9   7  1.51  10  0.75  molprobity  
32  32  t         -75.5   -40.4  Favored   9   7  1.25  10  0.80  molprobity  
33  33  ?         -60.0   -50.3  Favored   5   5  1.01   7  0.62  molprobity  
34  34  mttt      -61.7   -39.6  Favored  13   9  0.77  11  0.87  molprobity  
35  35  tm-20     -60.0   -40.1  Favored   6   9  1.61  12  0.80  molprobity  
36  36  mt        -62.2   -42.1  Favored  11   8  0.84  11  0.78  molprobity  
37  37  t         -65.1   -40.0  Favored   9   7  0.96  10  0.82  molprobity  
38  38  ?         -62.4   -16.5  Favored   5   5  0.98   7  0.79  molprobity  
39  39  m         -95.9   -37.5  Favored   5   6  0.98   8  0.69  molprobity  
40  40  t         -60.0   131.3  Favored   4   6  0.91   8  1.13  molprobity  
41  41  m-20      -77.5   -29.1  Favored   4   8  1.08  11  0.79  molprobity  
42  42  mttt      -76.4   -42.1  Favored  13   9  0.93  11  0.93  molprobity  
43  43  m         -80.0   -10.0  Favored   4   6  0.89   8  1.04  molprobity  
44  44  OUTLIER   -73.5   -66.5  Allowed   8   9  1.09  12  0.71  molprobity  
45  45  mt        -82.6   146.3  Favored  11   8  0.93  11  0.86  molprobity  
46  46  mttp          ?       ?  ?        13   8  0.73   8  0.83  molprobity  
47  47  m-85          ?       ?  ?        11  12  1.36  16  0.78  molprobity  
48  48  mt       -104.3   145.4  Favored  11   8  1.03  11  0.89  molprobity  
49  49  m-20      -60.0   -39.2  Favored   4   8  0.97  11  0.82  molprobity  
50  50  ?         -46.2   -15.7  Allowed   3   4  1.68   5  0.88  molprobity  
51  51  mt        -60.0   -40.0  Favored  11   8  0.87  11  0.89  molprobity  
52  52  OUTLIER   -59.2   -39.7  Favored   4   8  1.20  11  0.70  molprobity  
53  53  tttm      -62.7   -40.0  Favored  13   9  0.90  11  0.91  molprobity  
54  54  ?         -61.5   -35.4  Favored   5   5  1.00   7  0.63  molprobity  
55  55  mt-30     -60.1   -40.0  Favored   8   9  0.94  12  0.83  molprobity  
56  56  tt0       -61.4   -40.0  Favored   6   9  1.64  12  0.83  molprobity  
57  57  mt-10     -95.9     6.6  Favored   6   9  1.64  12  0.90  molprobity  
58  58  t         -51.1   -41.8  Favored   4   6  0.90   8  1.05  molprobity  
59  59  mt-10     -60.0   -36.0  Favored   6   9  1.65  12  0.80  molprobity  
60  60  tttm      -65.0   -39.5  Favored  13   9  0.88  11  0.79  molprobity  
61  61  m-85      -85.5   -12.2  Favored   9  13  1.30  18  1.10  molprobity  
62  62  OUTLIER    57.8  -134.7  Allowed   7  11  0.82  15  0.62  molprobity  
63  63  OUTLIER   -84.6    -3.9  Favored   5   6  0.96   8  0.76  molprobity  
64  64  m-20      -80.3    76.5  Favored   6   8  0.97  11  0.82  molprobity  
65  65  p-90      -70.0   -26.6  Favored  10  16  1.07  23  1.51  molprobity  
66  66  mtt180    -60.0   -41.0  Favored  13  11  1.24  14  1.08  molprobity  
67  67  ?         -66.0   -42.0  Favored   5   5  0.94   7  0.59  molprobity  
68  68  ttp       -62.3   -44.5  Favored   9   8  0.85  10  1.04  molprobity  
69  69  ?         -57.6   -39.7  Favored   5   5  0.99   7  0.60  molprobity  
70  70  OUTLIER   -66.2   -38.0  Favored   5   6  1.01   8  0.72  molprobity  
71  71  m-20      -70.0   -41.9  Favored   4   8  1.11  11  0.64  molprobity  
72  72  m-85      -95.5    -0.2  Favored   9  12  1.37  16  0.76  molprobity  
73  73  m120       53.2    47.1  Favored   6   8  0.93  11  0.81  molprobity  
74  74  mt       -113.4   150.7  Favored  11   8  1.15  12  0.75  molprobity  
75  75  Cg_endo   -70.3   154.1  Favored   7   8  0.83  12  0.45  molprobity  
76  76  Cg_exo    -43.4   -23.4  Allowed   7   8  0.85  11  0.70  molprobity  
77  77  t         -60.0   -50.7  Favored   9   7  1.52  10  0.76  molprobity  
78  78  t         -75.5   -40.4  Favored   9   7  1.22  10  0.80  molprobity  
79  79  ?         -60.0   -50.3  Favored   5   5  1.01   7  0.61  molprobity  
80  80  mttt      -61.7   -39.6  Favored  13   9  0.78  11  0.87  molprobity  
81  81  tm-20     -60.0   -40.0  Favored   6   9  1.62  12  0.80  molprobity  
82  82  mt        -62.2   -42.0  Favored  11   8  0.85  11  0.79  molprobity  
83  83  t         -65.2   -40.0  Favored   9   7  0.96  10  0.82  molprobity  
84  84  ?         -62.2   -17.1  Favored   5   5  0.93   7  0.77  molprobity  
85  85  m         -95.4   -37.4  Favored   5   6  0.99   8  0.68  molprobity  
86  86  t         -60.0   131.3  Favored   4   6  0.91   8  1.13  molprobity  
87  87  m-20      -77.5   -29.2  Favored   4   8  1.08  11  0.79  molprobity  
88  88  mttt      -76.4   -42.1  Favored  13   9  0.92  11  0.93  molprobity  
89  89  m         -80.0   -10.0  Favored   4   6  0.89   8  1.06  molprobity  
90  90  tp60      -73.5   -66.4  Allowed   8   9  1.09  12  0.74  molprobity  
91  91  mt        -82.6   146.3  Favored  11   8  0.92  11  0.86  molprobity  
92  92  mttp          ?       ?  ?        13   8  0.72   8  0.84  molprobity  
#
loop_
_pdbx_vrpt_instance_clashes.ordinal
_pdbx_vrpt_instance_clashes.instance_id
_pdbx_vrpt_instance_clashes.label_atom_id
_pdbx_vrpt_instance_clashes.cid
_pdbx_vrpt_instance_clashes.clashmag
_pdbx_vrpt_instance_clashes.dist
 1   3  O     1  0.52  2.42  
 2   3  C     2  0.48  2.66  
 3   5  N     1  0.52  2.42  
 4   5  N     2  0.48  2.66  
 5  13  O     3  0.61  2.34  
 6  13  O     4  0.47  2.67  
 7  16  ND1   3  0.61  2.34  
 8  16  ND1   5  0.55  2.53  
 9  16  N     5  0.55  2.53  
10  16  CE1   4  0.47  2.67  
11  23  O     6  0.43  2.52  
12  27  N     6  0.43  2.52  
13  38  O     7  0.61  2.32  
14  44  NE2   7  0.61  2.32  
15  49  O     8  0.52  2.42  
16  49  C     9  0.48  2.66  
17  51  N     8  0.52  2.42  
18  51  N     9  0.48  2.66  
19  59  O    10  0.61  2.34  
20  59  O    11  0.47  2.67  
21  62  ND1  10  0.61  2.34  
22  62  ND1  12  0.55  2.53  
23  62  N    12  0.55  2.53  
24  62  CE1  11  0.47  2.67  
25  69  O    13  0.42  2.52  
26  73  N    13  0.42  2.52  
27  84  O    14  0.46  2.33  
28  90  OE1  14  0.46  2.33  
#
loop_
_pdbx_vrpt_software.ordinal
_pdbx_vrpt_software.name
_pdbx_vrpt_software.version
_pdbx_vrpt_software.success_y_or_n
1  molprobity   4.02b-467                                                             Y  
2  mogul        unknown                                                               Y  
3  percentiles  "20191225.v01 (using entries in the PDB archive December 25th 2019)"  Y  
##
