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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 no bond length outliers.
Standard geometry: angle outliers ?

There are no bond angle outliers.
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
5.64
255

There are 255 clashes. The table below contains the detailed list of all clashes based on a MolProbity analysis. Bad clashes are >= 0.4 Angstrom. The output is limited to 100 rows.

Atom 1 Atom 2 Clash(Å) Model ID (Worst) Models (Total)
H:61:ASP:OD1
H:65:ARG:NH1
0.79
1
1
G:61:ASP:OD1
G:65:ARG:NH1
0.75
1
1
A:150:GLN:NE2
B:145:ASP:O
0.75
1
1
C:150:GLN:NE2
D:145:ASP:O
0.73
1
1
N:1:NAG:O3
O:1:NAG:O5
0.73
1
1
E:345:ASN:O
YA:161:HOH:O
0.71
1
1
F:179:VAL:O
YA:226:HOH:O
0.69
1
1
C:345:ASN:O
YA:167:HOH:O
0.69
1
1
MA:1:NAG:O4
NA:1:NAG:O7
0.69
1
1
D:226:GLN:N
D:226:GLN:OE1
0.69
1
1
E:163:GLU:OE2
F:315:ARG:NH1
0.68
1
1
C:246:SER:O
YA:177:HOH:O
0.68
1
1
B:150:GLN:NE2
C:145:ASP:O
0.68
1
1
F:171:ARG:NH2
F:200:ASP:O
0.67
1
1
C:301:CYS:O
YA:370:HOH:O
0.67
1
1
A:85:PRO:O
A:87:ALA:N
0.67
1
1
F:121:GLU:O
G:124:ARG:NH2
0.66
1
1
E:363:VAL:O
YA:268:HOH:O
0.66
1
1
C:85:PRO:O
C:87:ALA:N
0.66
1
1
A:363:VAL:O
YA:272:HOH:O
0.66
1
1
C:309:THR:O
YA:130:HOH:O
0.66
1
1
G:301:CYS:SG
YA:368:HOH:O
0.66
1
1
C:363:VAL:O
YA:273:HOH:O
0.65
1
1
B:121:GLU:O
C:124:ARG:NH2
0.65
1
1
H:363:VAL:O
YA:270:HOH:O
0.65
1
1
E:206:ILE:HD13
E:222:TYR:HB3
0.65
1
1
C:260:GLU:N
C:260:GLU:OE1
0.64
1
1
E:235:GLU:O
E:238:LYS:NZ
0.64
1
1
G:298:ASN:OD1
G:299:GLY:N
0.64
1
1
C:179:VAL:O
YA:224:HOH:O
0.64
1
1
D:290:ILE:O
YA:78:HOH:O
0.64
1
1
G:260:GLU:N
G:260:GLU:OE1
0.64
1
1
B:309:THR:O
YA:131:HOH:O
0.64
1
1
D:260:GLU:N
D:260:GLU:OE1
0.64
1
1
F:260:GLU:N
F:260:GLU:OE1
0.64
1
1
B:160:ALA:O
YA:172:HOH:O
0.64
1
1
A:242:GLU:N
A:242:GLU:OE1
0.63
1
1
H:260:GLU:N
H:260:GLU:OE1
0.63
1
1
E:260:GLU:N
E:260:GLU:OE1
0.63
1
1
DA:1:NAG:O3
EA:1:BMA:O5
0.63
1
1
T:1:BMA:O4
U:1:MAN:O5
0.63
1
1
E:179:VAL:O
YA:227:HOH:O
0.63
1
1
H:242:GLU:N
H:242:GLU:OE1
0.63
1
1
D:61:ASP:OD1
D:65:ARG:NH1
0.62
1
1
E:242:GLU:N
E:242:GLU:OE1
0.62
1
1
F:242:GLU:N
F:242:GLU:OE1
0.62
1
1
C:329:GLU:N
C:329:GLU:OE1
0.62
1
1
F:199:THR:OG1
YA:69:HOH:O
0.62
1
1
G:179:VAL:O
YA:230:HOH:O
0.62
1
1
A:329:GLU:N
A:329:GLU:OE1
0.62
1
1
B:260:GLU:N
B:260:GLU:OE1
0.62
1
1
A:297:LYS:O
H:213:LYS:NZ
0.62
1
1
C:258:ASN:OD1
C:259:SER:N
0.62
1
1
E:204:LYS:HE2
E:206:ILE:HD11
0.62
1
1
C:242:GLU:N
C:242:GLU:OE1
0.62
1
1
C:109:ASP:OD1
C:112:ARG:NH2
0.61
1
1
E:315:ARG:NH1
H:163:GLU:OE2
0.61
1
1
F:329:GLU:N
F:329:GLU:OE1
0.61
1
1
H:329:GLU:N
H:329:GLU:OE1
0.61
1
1
B:242:GLU:N
B:242:GLU:OE1
0.61
1
1
A:109:ASP:OD1
A:112:ARG:NH2
0.61
1
1
D:242:GLU:N
D:242:GLU:OE1
0.61
1
1
B:4:ASP:OD2
B:70:ARG:NH2
0.61
1
1
G:329:GLU:N
G:329:GLU:OE1
0.61
1
1
E:329:GLU:N
E:329:GLU:OE1
0.61
1
1
F:258:ASN:OD1
F:259:SER:N
0.61
1
1
G:347:VAL:HG13
G:352:THR:HG21
0.60
1
1
A:12:ASN:OD1
A:13:LEU:N
0.60
1
1
C:61:ASP:OD1
C:65:ARG:NH1
0.60
1
1
A:347:VAL:HG13
A:352:THR:HG21
0.60
1
1
G:38:GLU:N
G:38:GLU:OE1
0.60
1
1
F:170:MET:N
F:170:MET:SD
0.59
1
1
H:170:MET:N
H:170:MET:SD
0.59
1
1
G:258:ASN:OD1
G:259:SER:N
0.59
1
1
G:163:GLU:OE2
H:315:ARG:NH1
0.59
1
1
D:258:ASN:OD1
D:259:SER:N
0.59
1
1
H:38:GLU:N
H:38:GLU:OE1
0.59
1
1
F:347:VAL:HG13
F:352:THR:HG21
0.59
1
1
B:258:ASN:OD1
B:259:SER:N
0.59
1
1
E:258:ASN:OD1
E:259:SER:N
0.58
1
1
A:246:SER:O
YA:183:HOH:O
0.58
1
1
D:38:GLU:N
D:38:GLU:OE1
0.58
1
1
H:347:VAL:HG13
H:352:THR:HG21
0.58
1
1
A:315:ARG:NH1
D:163:GLU:OE2
0.57
1
1
B:215:ASN:ND2
B:218:GLU:OE2
0.57
1
1
C:38:GLU:N
C:38:GLU:OE1
0.57
1
1
F:319:PHE:CE2
F:347:VAL:HG11
0.57
1
1
H:79:ALA:O
H:83:ALA:N
0.57
1
1
A:319:PHE:CE2
A:347:VAL:HG11
0.57
1
1
C:213:LYS:NZ
F:297:LYS:O
0.57
1
1
E:145:ASP:O
H:150:GLN:NE2
0.56
1
1
H:319:PHE:CE2
H:347:VAL:HG11
0.56
1
1
C:347:VAL:HG13
C:352:THR:HG21
0.56
1
1
E:121:GLU:O
F:124:ARG:NH2
0.56
1
1
A:236:GLU:N
A:236:GLU:OE1
0.56
1
1
G:215:ASN:ND2
G:218:GLU:OE2
0.55
1
1
B:231:VAL:HG13
B:237:ASN:O
0.55
1
1
B:297:LYS:O
G:213:LYS:NZ
0.55
1
1
H:244:MET:N
H:244:MET:SD
0.55
1
1
A:231:VAL:HG13
A:237:ASN:O
0.55
1
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
2896
2542
321
33

There are 33 unique backbone outliers. Detailed list of outliers are tabulated below.

Chain Res Type Models (Total)
A
86
CYS
1
A
89
GLY
1
A
159
PRO
1
A
182
VAL
1
A
302
VAL
1
B
86
CYS
1
B
89
GLY
1
B
182
VAL
1
B
226
GLN
1
B
303
GLY
1
C
86
CYS
1
C
89
GLY
1
C
159
PRO
1
C
300
CYS
1
D
86
CYS
1
D
89
GLY
1
D
159
PRO
1
D
182
VAL
1
D
298
ASN
1
D
300
CYS
1
E
86
CYS
1
E
89
GLY
1
E
159
PRO
1
E
297
LYS
1
E
300
CYS
1
F
297
LYS
1
F
304
GLY
1
G
86
CYS
1
G
159
PRO
1
G
303
GLY
1
H
86
CYS
1
H
159
PRO
1
H
300
CYS
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
2360
2336
16
8

There are 8 unique sidechain outliers. Detailed list of outliers are tabulated below.

Chain Res Type Models (Total)
A
203
ASN
1
B
213
LYS
1
C
203
ASN
1
D
213
LYS
1
F
86
CYS
1
F
170
MET
1
H
170
MET
1
H
301
CYS
1