PDBIHM.org

PDB-IHM

System for Archiving Integrative Structures

Model quality ?

For models with atomic structures, MolProbity analysis is performed. For models with coarse-grained or multi-scale structures, excluded volume analysis is performed.

Standard geometry: bond outliers ?

There are 278 bond length outliers in this entry (0.69% of 40116 assessed bonds). A summary is provided below. The output is limited to 100 rows.

Chain Res Type Atoms |Z| Observed (Å) Ideal (Å) Model ID (Worst) Models (Total)
p
39
DG
N9-C4
26.60
0.85
1.38
1
1
q
28
DA
N9-C4
21.04
0.96
1.38
1
1
4
1371
SER
C-N
19.68
1.05
1.33
1
1
p
66
DA
N9-C8
17.97
1.73
1.37
1
1
q
158
DC
C2-O2
17.47
0.89
1.24
1
1
p
71
DG
N9-C8
16.54
1.70
1.37
1
1
q
160
DG
C5-C6
16.09
1.09
1.42
1
1
p
39
DG
C5-C6
15.92
1.10
1.42
1
1
p
39
DG
C2-N3
15.65
1.64
1.33
1
1
q
160
DG
N7-C5
14.65
1.68
1.39
1
1
q
126
DC
N1-C2
14.46
1.11
1.40
1
1
q
157
DA
N9-C8
14.31
1.65
1.37
1
1
q
158
DC
C4'-O4'
13.89
1.73
1.45
1
1
q
126
DC
N3-C4
13.85
1.61
1.33
1
1
p
40
DT
N3-C4
13.69
1.66
1.38
1
1
p
65
DC
N1-C6
13.15
1.10
1.36
1
1
p
40
DT
C4-C5
13.14
1.70
1.44
1
1
q
160
DG
N9-C4
13.13
1.11
1.38
1
1
p
40
DT
C2-N3
13.06
1.11
1.37
1
1
p
66
DA
C5-C6
13.01
1.15
1.41
1
1
p
37
DC
N3-C4
12.98
1.59
1.33
1
1
q
164
DT
N1-C2
12.93
1.12
1.38
1
1
p
39
DG
C2'-C1'
12.90
1.27
1.52
1
1
q
132
DG
N9-C8
12.71
1.63
1.37
1
1
p
37
DC
C4-C5
12.58
1.68
1.43
1
1
q
160
DG
C8-N7
12.43
1.06
1.30
1
1
p
71
DG
N9-C4
12.42
1.13
1.38
1
1
q
28
DA
C1'-N9
11.74
1.69
1.46
1
1
p
37
DC
C5-C6
11.72
1.10
1.34
1
1
q
158
DC
N3-C4
11.46
1.56
1.33
1
1
q
158
DC
C5-C6
11.43
1.11
1.34
1
1
q
158
DC
C4-C5
11.33
1.65
1.43
1
1
q
126
DC
C4-C5
10.86
1.64
1.43
1
1
p
39
DG
N3-C4
10.84
1.57
1.35
1
1
p
37
DC
N1-C2
10.67
1.19
1.40
1
1
q
126
DC
C2-N3
10.64
1.14
1.36
1
1
q
164
DT
C5-C6
10.60
1.13
1.34
1
1
4
1191
HIS
CB-CG
10.54
1.35
1.50
1
1
p
37
DC
N1-C6
10.46
1.15
1.36
1
1
p
65
DC
C4-C5
10.38
1.63
1.43
1
1
p
39
DG
C5-C4
10.26
1.17
1.38
1
1
p
66
DA
C6-N6
10.19
1.13
1.34
1
1
4
445
GLN
C-N
10.14
1.47
1.33
1
1
q
157
DA
C5-C6
10.12
1.21
1.41
1
1
p
66
DA
C8-N7
10.02
1.11
1.31
1
1
p
33
DA
N9-C8
10.02
1.57
1.37
1
1
q
159
DC
C4-N4
9.93
1.14
1.34
1
1
p
65
DC
N1-C2
9.85
1.20
1.40
1
1
p
39
DG
O4'-C1'
9.81
1.61
1.41
1
1
p
169
DT
N1-C6
9.50
1.19
1.38
1
1
q
158
DC
C2-N3
9.48
1.17
1.36
1
1
p
169
DT
C4-C5
9.43
1.63
1.44
1
1
p
169
DT
N1-C2
9.35
1.19
1.38
1
1
p
65
DC
N3-C4
9.32
1.52
1.33
1
1
1
538
GLN
CG-CD
9.27
1.28
1.52
1
1
q
159
DC
C4-C5
9.26
1.61
1.43
1
1
q
160
DG
C5-C4
9.24
1.19
1.38
1
1
p
41
DC
N1-C2
9.13
1.22
1.40
1
1
P
86
HIS
CB-CG
8.94
1.62
1.50
1
1
q
131
DT
N1-C6
8.93
1.20
1.38
1
1
b
163
THR
C-N
8.62
1.45
1.33
1
1
p
33
DA
C8-N7
8.52
1.14
1.31
1
1
q
28
DA
N9-C8
8.48
1.54
1.37
1
1
q
157
DA
C8-N7
8.34
1.15
1.31
1
1
p
65
DC
C2-N3
8.23
1.19
1.36
1
1
4
1073
LEU
CG-CD2
8.22
1.25
1.52
1
1
p
38
DG
N1-C2
8.18
1.21
1.38
1
1
q
28
DA
N7-C5
8.15
1.22
1.39
1
1
A
1816
ILE
CB-CG2
8.12
1.25
1.52
1
1
p
40
DT
N1-C2
8.09
1.22
1.38
1
1
p
39
DG
C6-N1
8.01
1.23
1.39
1
1
p
71
DG
C8-N7
7.94
1.15
1.30
1
1
p
39
DG
C6-O6
7.94
1.08
1.24
1
1
6
283
PRO
N-CD
7.78
1.36
1.47
1
1
q
131
DT
N1-C2
7.78
1.22
1.38
1
1
p
39
DG
N1-C2
7.74
1.53
1.38
1
1
q
160
DG
O4'-C1'
7.70
1.26
1.41
1
1
p
33
DA
N9-C4
7.64
1.22
1.38
1
1
p
40
DT
C2-O2
7.54
1.07
1.22
1
1
p
71
DG
N7-C5
7.50
1.24
1.39
1
1
b
164
PHE
N-CA
7.49
1.60
1.46
1
1
4
1212
GLU
CG-CD
7.40
1.33
1.52
1
1
4
1085
LEU
CB-CG
7.29
1.38
1.53
1
1
q
28
DA
O4'-C1'
7.28
1.56
1.41
1
1
p
169
DT
N3-C4
7.20
1.53
1.38
1
1
X
67
PRO
N-CD
7.09
1.37
1.47
1
1
p
71
DG
C5-C4
7.06
1.52
1.38
1
1
B
8
LEU
CB-CG
6.97
1.67
1.53
1
1
A
1818
GLN
CA-C
6.85
1.67
1.52
1
1
A
2049
TRP
CD2-CE3
6.79
1.51
1.40
1
1
4
918
LEU
CB-CG
6.77
1.67
1.53
1
1
1
537
TYR
CB-CG
6.60
1.66
1.51
1
1
V
27
PRO
N-CD
6.54
1.38
1.47
1
1
q
28
DA
C8-N7
6.54
1.18
1.31
1
1
q
132
DG
N9-C4
6.53
1.25
1.38
1
1
q
159
DC
C2-O2
6.49
1.11
1.24
1
1
b
385
TRP
CZ2-CH2
6.46
1.49
1.37
1
1
v
27
PRO
N-CD
6.45
1.38
1.47
1
1
p
38
DG
C5-C4
6.42
1.51
1.38
1
1
b
385
TRP
CD2-CE3
6.41
1.50
1.40
1
1

Standard geometry: angle outliers ?

There are 547 bond angle outliers in this entry (0.99% of 55397 assessed bonds). A summary is provided below. The output is limited to 100 rows.

Chain Res Type Atoms |Z| Observed (Å) Ideal (Å) Model ID (Worst) Models (Total)
p
40
DT
O2-C2-N3
80.76
0.86
122.00
1
1
p
33
DA
N9-C4-C5
61.76
13.06
105.70
1
1
q
160
DG
C8-N7-C5
58.32
16.72
104.20
1
1
q
158
DC
O2-C2-N3
56.52
37.13
121.90
1
1
p
66
DA
N9-C4-C5
51.59
28.32
105.70
1
1
p
37
DC
N1-C2-O2
51.12
42.51
119.20
1
1
p
71
DG
N9-C4-C5
50.43
29.96
105.60
1
1
q
132
DG
N9-C4-C5
50.29
30.16
105.60
1
1
p
37
DC
O2-C2-N3
50.07
46.80
121.90
1
1
q
157
DA
N9-C4-C5
50.00
30.70
105.70
1
1
q
158
DC
N1-C2-O2
49.96
44.26
119.20
1
1
p
65
DC
O2-C2-N3
49.69
47.36
121.90
1
1
p
169
DT
O2-C2-N3
48.98
48.54
122.00
1
1
q
160
DG
N9-C4-C5
47.98
33.63
105.60
1
1
q
126
DC
O2-C2-N3
47.11
51.23
121.90
1
1
p
169
DT
N1-C2-O2
46.98
52.73
123.20
1
1
q
126
DC
N1-C2-O2
44.96
51.76
119.20
1
1
q
131
DT
N1-C2-O2
44.06
57.11
123.20
1
1
q
28
DA
N9-C4-C5
43.94
39.79
105.70
1
1
q
131
DT
O2-C2-N3
43.88
56.18
122.00
1
1
q
164
DT
N1-C2-N3
42.13
51.60
114.80
1
1
p
39
DG
N9-C4-C5
41.68
43.08
105.60
1
1
p
39
DG
C8-N7-C5
39.91
44.34
104.20
1
1
q
28
DA
C8-N7-C5
39.08
45.28
103.90
1
1
p
65
DC
N1-C2-O2
38.12
62.03
119.20
1
1
p
39
DG
C8-N9-C4
37.94
49.09
106.00
1
1
q
160
DG
C1'-N9-C4
37.03
71.46
127.00
1
1
p
66
DA
C8-N9-C4
36.28
51.48
105.90
1
1
p
40
DT
N1-C6-C5
36.25
68.43
122.80
1
1
q
157
DA
C8-N9-C4
35.70
52.35
105.90
1
1
q
132
DG
C8-N9-C4
34.92
53.62
106.00
1
1
q
132
DG
C8-N7-C5
34.22
52.87
104.20
1
1
q
160
DG
N9-C4-N3
33.57
176.35
126.00
1
1
q
164
DT
O2-C2-N3
33.03
72.46
122.00
1
1
q
28
DA
C1'-N9-C4
32.82
176.28
127.05
1
1
q
157
DA
C1'-N9-C8
32.51
175.82
127.05
1
1
q
157
DA
C8-N7-C5
32.03
55.86
103.90
1
1
q
126
DC
N1-C6-C5
31.89
73.16
121.00
1
1
p
66
DA
C8-N7-C5
31.60
56.49
103.90
1
1
q
160
DG
C2-N3-C4
29.78
67.12
111.80
1
1
p
71
DG
C8-N9-C4
29.34
61.99
106.00
1
1
q
131
DT
C1'-N1-C6
29.12
75.68
119.35
1
1
p
65
DC
N1-C6-C5
28.67
77.99
121.00
1
1
p
39
DG
N9-C4-N3
28.15
83.78
126.00
1
1
p
169
DT
N1-C6-C5
27.95
80.88
122.80
1
1
p
71
DG
C8-N7-C5
27.85
62.42
104.20
1
1
q
28
DA
C8-N9-C4
27.85
64.13
105.90
1
1
p
169
DT
C2-N1-C6
27.80
162.99
121.30
1
1
q
131
DT
C1'-N1-C2
27.24
78.49
119.35
1
1
q
158
DC
N1-C6-C5
27.15
80.28
121.00
1
1
q
132
DG
C1'-N9-C8
26.74
86.90
127.00
1
1
p
37
DC
N1-C6-C5
26.59
81.11
121.00
1
1
p
33
DA
C8-N7-C5
25.34
65.89
103.90
1
1
q
158
DC
N1-C2-N3
25.01
81.38
118.90
1
1
p
65
DC
C2-N1-C6
24.86
157.89
120.60
1
1
p
33
DA
N9-C8-N7
24.68
76.78
113.80
1
1
q
126
DC
C2-N3-C4
22.87
85.70
120.00
1
1
q
131
DT
C2-N1-C6
21.91
154.17
121.30
1
1
p
40
DT
N1-C2-O2
21.13
91.51
123.20
1
1
p
40
DT
C2-N3-C4
21.02
95.47
127.00
1
1
p
39
DG
C1'-N9-C4
20.80
158.20
127.00
1
1
p
37
DC
C2-N3-C4
20.69
88.97
120.00
1
1
p
33
DA
C8-N9-C4
20.25
75.53
105.90
1
1
p
39
DG
N7-C5-C6
19.89
100.26
130.10
1
1
p
66
DA
C1'-N9-C4
19.74
97.44
127.05
1
1
p
37
DC
N1-C2-N3
19.72
89.31
118.90
1
1
p
66
DA
N9-C8-N7
19.59
84.41
113.80
1
1
q
28
DA
C5-C4-N3
19.54
156.21
126.90
1
1
p
71
DG
C1'-N9-C8
19.42
156.13
127.00
1
1
q
158
DC
C3'-O3'-P
19.36
149.24
120.20
1
1
p
65
DC
C2-N3-C4
19.32
91.02
120.00
1
1
q
164
DT
C2-N1-C6
19.30
150.25
121.30
1
1
D
471
GLY
C-N-CA
18.02
154.14
121.70
1
1
q
160
DG
N7-C5-C4
17.77
137.45
110.80
1
1
q
159
DC
C1'-N1-C6
17.66
146.19
119.70
1
1
q
160
DG
C8-N9-C4
17.65
79.52
106.00
1
1
p
65
DC
C1'-N1-C2
17.58
93.32
119.70
1
1
q
132
DG
N9-C4-N3
17.53
99.71
126.00
1
1
q
28
DA
N7-C5-C4
17.52
136.98
110.70
1
1
p
71
DG
N9-C8-N7
17.41
87.38
113.50
1
1
q
160
DG
N9-C8-N7
16.99
138.98
113.50
1
1
A
1923
THR
C-N-CA
16.96
152.23
121.70
1
1
q
157
DA
N9-C8-N7
16.79
88.62
113.80
1
1
q
160
DG
C6-C5-C4
16.76
93.96
119.10
1
1
q
164
DT
C4-C5-C6
16.52
94.42
119.20
1
1
p
38
DG
N9-C4-N3
16.44
150.65
126.00
1
1
D
350
GLN
C-N-CA
16.26
150.97
121.70
1
1
q
158
DC
C4'-O4'-C1'
16.09
85.57
109.70
1
1
q
160
DG
C1'-N9-C8
15.98
150.97
127.00
1
1
q
132
DG
N9-C8-N7
15.75
89.87
113.50
1
1
p
169
DT
C2-N3-C4
15.65
103.53
127.00
1
1
4
445
GLN
O-C-N
15.34
147.55
123.00
1
1
q
158
DC
C2-N3-C4
15.24
97.13
120.00
1
1
q
131
DT
N1-C6-C5
15.17
100.04
122.80
1
1
p
169
DT
C1'-N1-C2
15.15
96.62
119.35
1
1
p
40
DT
N1-C2-N3
14.95
92.37
114.80
1
1
4
445
GLN
CA-C-N
14.86
86.48
116.20
1
1
p
66
DA
C1'-N9-C8
14.58
148.92
127.05
1
1
q
160
DG
C5-C4-N3
14.41
150.02
128.40
1
1
p
39
DG
C5-C6-N1
14.18
132.97
111.70
1
1

Too-close contacts ?

The following all-atom clashscore is based on a MolProbity analysis. All-atom clashscore is defined as the number of clashes found per 1000 atoms (including hydrogen atoms). The table below contains clashscores for all atomic models in this entry.

Model ID Clash score Number of clashes
1
0.00
0

There are no too-close contacts.
Torsion angles: Protein backbone ?

In the following table, Ramachandran outliers are listed. The Analysed column shows the number of residues for which the backbone conformation was analysed.

Model ID Analysed Favored Allowed Outliers
1
4036
3849
160
27

There are 27 unique backbone outliers. Detailed list of outliers are tabulated below.

Chain Res Type Models (Total)
4
718
TYR
1
4
957
ASN
1
4
984
VAL
1
4
1073
LEU
1
4
1289
PRO
1
4
1372
ARG
1
4
1382
SER
1
4
1383
LEU
1
6
71
ASP
1
A
1704
PHE
1
A
1823
PHE
1
A
1826
ASP
1
A
1935
GLU
1
A
2006
GLY
1
A
2074
SER
1
A
2211
SER
1
A
2222
PRO
1
P
75
PRO
1
b
132
VAL
1
b
147
CYS
1
b
153
ARG
1
b
163
THR
1
b
168
PHE
1
b
257
GLN
1
b
303
LEU
1
b
330
GLU
1
b
355
THR
1

Torsion angles : Protein sidechains ?
In the following table, sidechain rotameric outliers are listed. The Analysed column shows the number of residues for which the sidechain conformation was analysed.

Model ID Analysed Favored Allowed Outliers
1
3557
3516
31
10

There are 10 unique sidechain outliers. Detailed list of outliers are tabulated below.

Chain Res Type Models (Total)
1
537
TYR
1
4
1014
LYS
1
4
1074
ASP
1
4
1362
GLU
1
4
1367
PHE
1
4
1375
LYS
1
4
1376
GLU
1
4
1377
VAL
1
A
1834
VAL
1
A
2124
LYS
1