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 52 bond length outliers in this entry (0.23% of 22825 assessed bonds). A summary is provided below.

Chain Res Type Atoms |Z| Observed (Å) Ideal (Å) Model ID (Worst) Models (Total)
T
37
VAL
C-N
12.23
1.16
1.33
1
1
P
35
VAL
C-N
11.49
1.49
1.33
1
1
N
35
VAL
C-N
11.45
1.49
1.33
1
1
J
35
VAL
C-N
11.45
1.49
1.33
1
1
E
35
VAL
C-N
11.43
1.49
1.33
1
1
H
35
VAL
C-N
11.42
1.49
1.33
1
1
O
35
VAL
C-N
11.40
1.49
1.33
1
1
F
35
VAL
C-N
11.39
1.49
1.33
1
1
G
35
VAL
C-N
11.39
1.49
1.33
1
1
K
35
VAL
C-N
11.37
1.49
1.33
1
1
C
35
VAL
C-N
11.37
1.49
1.33
1
1
M
35
VAL
C-N
11.37
1.49
1.33
1
1
I
35
VAL
C-N
11.37
1.49
1.33
1
1
L
35
VAL
C-N
11.36
1.49
1.33
1
1
A
35
VAL
C-N
11.36
1.49
1.33
1
1
D
35
VAL
C-N
11.32
1.49
1.33
1
1
B
35
VAL
C-N
11.27
1.49
1.33
1
1
H
36
ALA
C-N
7.61
1.44
1.33
1
1
D
36
ALA
C-N
7.57
1.44
1.33
1
1
O
36
ALA
C-N
7.56
1.43
1.33
1
1
M
36
ALA
C-N
7.56
1.43
1.33
1
1
G
36
ALA
C-N
7.55
1.43
1.33
1
1
S
37
GLN
C-N
7.54
1.22
1.33
1
1
K
36
ALA
C-N
7.54
1.43
1.33
1
1
N
36
ALA
C-N
7.53
1.43
1.33
1
1
F
36
ALA
C-N
7.53
1.43
1.33
1
1
P
36
ALA
C-N
7.53
1.43
1.33
1
1
E
36
ALA
C-N
7.52
1.43
1.33
1
1
B
36
ALA
C-N
7.51
1.43
1.33
1
1
A
36
ALA
C-N
7.51
1.43
1.33
1
1
I
36
ALA
C-N
7.50
1.43
1.33
1
1
C
36
ALA
C-N
7.49
1.43
1.33
1
1
L
36
ALA
C-N
7.47
1.43
1.33
1
1
J
36
ALA
C-N
7.45
1.43
1.33
1
1
O
131
ASN
C-N
4.65
1.26
1.33
1
1
A
131
ASN
C-N
4.65
1.26
1.33
1
1
L
131
ASN
C-N
4.63
1.26
1.33
1
1
G
131
ASN
C-N
4.62
1.26
1.33
1
1
H
131
ASN
C-N
4.60
1.26
1.33
1
1
K
131
ASN
C-N
4.60
1.26
1.33
1
1
J
131
ASN
C-N
4.60
1.26
1.33
1
1
M
131
ASN
C-N
4.59
1.26
1.33
1
1
I
131
ASN
C-N
4.58
1.26
1.33
1
1
N
131
ASN
C-N
4.57
1.26
1.33
1
1
C
131
ASN
C-N
4.57
1.27
1.33
1
1
E
131
ASN
C-N
4.56
1.27
1.33
1
1
B
131
ASN
C-N
4.56
1.27
1.33
1
1
P
131
ASN
C-N
4.54
1.27
1.33
1
1
F
131
ASN
C-N
4.52
1.27
1.33
1
1
P
28
PRO
N-CD
4.51
1.54
1.47
1
1
D
131
ASN
C-N
4.44
1.27
1.33
1
1
O
28
PRO
N-CD
4.28
1.53
1.47
1
1

Standard geometry: angle outliers ?

There are 85 bond angle outliers in this entry (0.27% of 31052 assessed bonds). A summary is provided below.

Chain Res Type Atoms |Z| Observed (Å) Ideal (Å) Model ID (Worst) Models (Total)
S
37
GLN
C-N-CA
25.16
76.40
121.70
1
1
S
37
GLN
O-C-N
20.46
155.73
123.00
1
1
R
3
LEU
O-C-N
18.74
93.01
123.00
1
1
T
37
VAL
O-C-N
15.68
97.92
123.00
1
1
S
37
GLN
CA-C-N
14.55
87.10
116.20
1
1
R
3
LEU
CA-C-N
11.49
139.18
116.20
1
1
P
36
ALA
C-N-CA
10.31
103.14
121.70
1
1
N
36
ALA
C-N-CA
10.30
103.17
121.70
1
1
H
36
ALA
C-N-CA
10.29
103.18
121.70
1
1
C
36
ALA
C-N-CA
10.28
103.19
121.70
1
1
O
36
ALA
C-N-CA
10.28
103.19
121.70
1
1
M
36
ALA
C-N-CA
10.28
103.19
121.70
1
1
A
36
ALA
C-N-CA
10.28
103.20
121.70
1
1
F
36
ALA
C-N-CA
10.28
103.20
121.70
1
1
D
36
ALA
C-N-CA
10.27
103.21
121.70
1
1
G
36
ALA
C-N-CA
10.26
103.22
121.70
1
1
K
36
ALA
C-N-CA
10.26
103.23
121.70
1
1
I
36
ALA
C-N-CA
10.26
103.23
121.70
1
1
B
36
ALA
C-N-CA
10.26
103.23
121.70
1
1
J
36
ALA
C-N-CA
10.26
103.24
121.70
1
1
E
36
ALA
C-N-CA
10.25
103.25
121.70
1
1
L
36
ALA
C-N-CA
10.25
103.25
121.70
1
1
T
37
VAL
CA-C-N
6.03
128.27
116.20
1
1
P
36
ALA
O-C-N
5.62
131.99
123.00
1
1
A
36
ALA
O-C-N
5.58
131.93
123.00
1
1
L
36
ALA
O-C-N
5.57
131.92
123.00
1
1
F
36
ALA
O-C-N
5.57
131.92
123.00
1
1
H
36
ALA
O-C-N
5.57
131.91
123.00
1
1
N
36
ALA
O-C-N
5.56
131.90
123.00
1
1
M
36
ALA
O-C-N
5.56
131.90
123.00
1
1
J
36
ALA
O-C-N
5.56
131.89
123.00
1
1
S
32
GLN
CA-C-N
5.55
127.31
116.20
1
1
B
36
ALA
O-C-N
5.54
131.87
123.00
1
1
D
36
ALA
O-C-N
5.54
131.86
123.00
1
1
G
36
ALA
O-C-N
5.54
131.86
123.00
1
1
O
36
ALA
O-C-N
5.54
131.86
123.00
1
1
C
36
ALA
O-C-N
5.53
131.85
123.00
1
1
I
36
ALA
O-C-N
5.52
131.83
123.00
1
1
S
14
ALA
CA-C-N
5.51
127.23
116.20
1
1
E
36
ALA
O-C-N
5.51
131.82
123.00
1
1
K
36
ALA
O-C-N
5.50
131.80
123.00
1
1
G
36
ALA
CA-C-N
5.49
105.22
116.20
1
1
F
36
ALA
CA-C-N
5.49
105.22
116.20
1
1
M
36
ALA
CA-C-N
5.49
105.23
116.20
1
1
L
36
ALA
CA-C-N
5.48
105.23
116.20
1
1
O
36
ALA
CA-C-N
5.48
105.24
116.20
1
1
A
36
ALA
CA-C-N
5.47
105.25
116.20
1
1
H
36
ALA
CA-C-N
5.47
105.26
116.20
1
1
N
36
ALA
CA-C-N
5.47
105.26
116.20
1
1
P
36
ALA
CA-C-N
5.47
105.27
116.20
1
1
D
36
ALA
CA-C-N
5.46
105.27
116.20
1
1
E
36
ALA
CA-C-N
5.46
105.28
116.20
1
1
C
36
ALA
CA-C-N
5.46
105.28
116.20
1
1
K
36
ALA
CA-C-N
5.46
105.28
116.20
1
1
I
36
ALA
CA-C-N
5.46
105.29
116.20
1
1
B
36
ALA
CA-C-N
5.44
105.32
116.20
1
1
R
14
ALA
CA-C-N
5.44
127.08
116.20
1
1
J
36
ALA
CA-C-N
5.43
105.34
116.20
1
1
S
32
GLN
O-C-N
5.23
114.62
123.00
1
1
S
21
TYR
CA-C-N
5.01
126.21
116.20
1
1
R
21
LEU
CA-C-N
4.99
126.18
116.20
1
1
S
19
ALA
N-CA-CB
4.97
102.94
110.40
1
1
S
19
ALA
C-CA-CB
4.92
117.88
110.50
1
1
O
29
ASP
CA-CB-CG
4.65
107.95
112.60
1
1
R
13
PHE
CA-C-N
4.39
124.98
116.20
1
1
H
102
ALA
C-CA-CB
4.37
117.05
110.50
1
1
L
102
ALA
C-CA-CB
4.37
117.05
110.50
1
1
F
102
ALA
C-CA-CB
4.37
117.05
110.50
1
1
B
102
ALA
C-CA-CB
4.34
117.01
110.50
1
1
A
102
ALA
C-CA-CB
4.33
117.00
110.50
1
1
C
102
ALA
C-CA-CB
4.33
116.99
110.50
1
1
J
102
ALA
C-CA-CB
4.33
116.99
110.50
1
1
K
102
ALA
C-CA-CB
4.33
116.99
110.50
1
1
D
102
ALA
C-CA-CB
4.32
116.98
110.50
1
1
I
102
ALA
C-CA-CB
4.32
116.98
110.50
1
1
O
102
ALA
C-CA-CB
4.31
116.96
110.50
1
1
N
102
ALA
C-CA-CB
4.31
116.96
110.50
1
1
G
102
ALA
C-CA-CB
4.30
116.96
110.50
1
1
E
102
ALA
C-CA-CB
4.30
116.95
110.50
1
1
P
102
ALA
C-CA-CB
4.30
116.94
110.50
1
1
S
13
PHE
CA-C-N
4.29
124.79
116.20
1
1
M
102
ALA
C-CA-CB
4.29
116.93
110.50
1
1
R
21
LEU
O-C-N
4.07
116.49
123.00
1
1
T
2
ALA
C-N-CA
4.06
114.39
121.70
1
1
R
14
ALA
O-C-N
4.01
116.59
123.00
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
2842
2675
148
19

There are 19 unique backbone outliers. Detailed list of outliers are tabulated below.

Chain Res Type Models (Total)
C
102
ALA
1
E
22
PRO
1
E
55
PHE
1
F
22
PRO
1
G
22
PRO
1
I
22
PRO
1
J
22
PRO
1
K
22
PRO
1
K
55
PHE
1
L
22
PRO
1
M
22
PRO
1
M
55
PHE
1
N
55
PHE
1
O
22
PRO
1
O
55
PHE
1
P
22
PRO
1
P
55
PHE
1
Q
78
ARG
1
S
4
LEU
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
2357
2299
45
13

There are 13 unique sidechain outliers. Detailed list of outliers are tabulated below.

Chain Res Type Models (Total)
D
92
ASP
1
E
92
ASP
1
F
9
VAL
1
G
9
VAL
1
G
88
LYS
1
G
92
ASP
1
H
92
ASP
1
I
92
ASP
1
J
92
ASP
1
L
92
ASP
1
M
92
ASP
1
O
9
VAL
1
P
92
ASP
1