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 34 bond length outliers in this entry (0.44% of 7680 assessed bonds). A summary is provided below.

Chain Res Type Atoms |Z| Observed (Å) Ideal (Å) Model ID (Worst) Models (Total)
A
178
PRO
N-CD
8.78
1.60
1.47
4
5
A
183
PRO
N-CD
8.33
1.59
1.47
2
5
A
102
PRO
N-CD
5.47
1.55
1.47
5
5
A
81
PRO
N-CD
5.38
1.55
1.47
4
5
A
98
PRO
N-CD
5.03
1.54
1.47
1
4
A
165
PRO
N-CD
4.90
1.54
1.47
5
5
A
138
PRO
N-CD
4.71
1.54
1.47
1
3
A
23
PRO
N-CD
4.06
1.53
1.47
1
2

Standard geometry: angle outliers ?

There are 55 bond angle outliers in this entry (0.53% of 10370 assessed bonds). A summary is provided below.

Chain Res Type Atoms |Z| Observed (Å) Ideal (Å) Model ID (Worst) Models (Total)
A
88
CYS
N-CA-CB
4.60
102.68
110.50
1
5
A
168
CYS
N-CA-CB
4.59
102.70
110.50
3
5
A
64
CYS
N-CA-CB
4.59
102.70
110.50
4
5
A
52
CYS
N-CA-CB
4.58
102.71
110.50
4
5
A
77
CYS
N-CA-CB
4.58
102.71
110.50
4
5
A
44
CYS
N-CA-CB
4.58
102.71
110.50
4
5
A
159
CYS
N-CA-CB
4.58
102.72
110.50
4
5
A
45
CYS
N-CA-CB
4.57
102.72
110.50
5
5
A
115
CYS
N-CA-CB
4.57
102.73
110.50
1
5
A
160
CYS
N-CA-CB
4.57
102.74
110.50
4
5
A
78
CYS
N-CA-CB
4.57
102.74
110.50
1
5

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
5.69
17
2
1.67
5
3
4.02
12
4
2.34
7
5
3.01
9

There are 50 clashes. The table below contains the detailed list of all clashes based on a MolProbity analysis. Bad clashes are >= 0.4 Angstrom.

Atom 1 Atom 2 Clash(Å) Model ID (Worst) Models (Total)
A:49:LEU:O
A:52:CYS:SG
0.69
4
1
A:122:LYS:H
A:122:LYS:HD2
0.61
1
1
A:61:LYS:HA
A:64:CYS:SG
0.58
5
1
A:157:GLU:O
A:160:CYS:SG
0.57
3
1
A:50:LEU:O
A:50:LEU:HD23
0.56
4
1
A:37:LEU:O
A:37:LEU:HD23
0.53
1
1
A:41:HIS:HE1
A:52:CYS:SG
0.53
3
1
A:37:LEU:C
A:37:LEU:HD23
0.52
1
1
A:182:GLU:HB2
A:183:PRO:HD3
0.52
1
2
A:122:LYS:HD2
A:122:LYS:N
0.52
1
1
A:177:LYS:N
A:178:PRO:CD
0.52
3
3
A:122:LYS:CD
A:122:LYS:H
0.51
1
1
A:111:SER:O
A:115:CYS:SG
0.50
1
2
A:182:GLU:N
A:183:PRO:CD
0.49
4
4
A:85:LYS:O
A:88:CYS:SG
0.49
2
2
A:125:PHE:HD1
A:125:PHE:O
0.49
1
1
A:112:LYS:O
A:115:CYS:SG
0.49
4
2
A:74:LEU:O
A:78:CYS:SG
0.48
3
1
A:182:GLU:HB3
A:183:PRO:HD3
0.47
4
3
A:75:LYS:HA
A:78:CYS:SG
0.47
5
1
A:133:TYR:HD1
A:133:TYR:O
0.46
1
1
A:177:LYS:HB3
A:178:PRO:HD3
0.45
2
3
A:41:HIS:CE1
A:52:CYS:SG
0.45
3
1
A:84:GLU:O
A:88:CYS:SG
0.45
4
2
A:75:LYS:O
A:78:CYS:SG
0.45
5
1
A:164:ASP:O
A:168:CYS:SG
0.44
1
1
A:156:LEU:O
A:159:CYS:HB2
0.44
1
1
A:18:LEU:HD23
A:59:LEU:HD21
0.43
3
1
A:156:LEU:HA
A:156:LEU:HD12
0.43
1
1
A:125:PHE:C
A:125:PHE:CD1
0.43
1
1
A:50:LEU:CD2
A:50:LEU:O
0.42
4
1
A:155:THR:O
A:159:CYS:SG
0.42
3
1
A:2:LEU:O
A:2:LEU:HD23
0.41
5
1
A:41:HIS:HA
A:44:CYS:HB2
0.41
5
1
A:177:LYS:N
A:178:PRO:HD2
0.41
2
1
A:2:LEU:C
A:2:LEU:HD23
0.40
5
1

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
187
184
3
0
2
187
186
1
0
3
187
186
1
0
4
187
182
5
0
5
187
185
2
0

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
165
157
4
4
2
165
165
0
0
3
165
161
3
1
4
165
162
1
2
5
165
163
1
1

There are 6 unique sidechain outliers. Detailed list of outliers are tabulated below.

Chain Res Type Models (Total)
A
18
LEU
3
A
50
LEU
1
A
59
LEU
1
A
74
LEU
1
A
130
LEU
1
A
156
LEU
1