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 63 bond length outliers in this entry (0.86% of 7323 assessed bonds). A summary is provided below.

Chain Res Type Atoms |Z| Observed (Å) Ideal (Å) Model ID (Worst) Models (Total)
C
477
TPO
OG1-P
9.76
1.52
1.72
1
1
C
467
SEP
O2P-P
4.85
1.51
1.61
1
1
C
478
SEP
O1P-P
4.85
1.51
1.61
1
1
C
463
SEP
O1P-P
4.83
1.51
1.61
1
1
C
467
SEP
O1P-P
4.82
1.51
1.61
1
1
C
493
SEP
O1P-P
4.81
1.51
1.61
1
1
C
493
SEP
O2P-P
4.80
1.51
1.61
1
1
C
463
SEP
O2P-P
4.79
1.51
1.61
1
1
C
467
SEP
O3P-P
4.79
1.51
1.61
1
1
C
478
SEP
O3P-P
4.78
1.51
1.61
1
1
C
463
SEP
O3P-P
4.78
1.51
1.61
1
1
C
493
SEP
O3P-P
4.77
1.51
1.61
1
1
C
478
SEP
O2P-P
4.75
1.52
1.61
1
1
C
493
SEP
OG-P
4.41
1.52
1.61
1
1
C
467
SEP
OG-P
4.40
1.52
1.61
1
1
C
478
SEP
OG-P
4.39
1.52
1.61
1
1
C
463
SEP
OG-P
4.37
1.52
1.61
1
1
C
476
HIS
CE1-NE2
4.36
1.36
1.32
1
1
C
394
HIS
CE1-NE2
4.34
1.36
1.32
1
1
A
198
HIS
CE1-NE2
4.34
1.36
1.32
1
1
C
199
HIS
CE1-NE2
4.34
1.36
1.32
1
1
A
353
HIS
CD2-NE2
4.33
1.33
1.37
1
1
C
197
HIS
CE1-NE2
4.33
1.36
1.32
1
1
A
111
HIS
CE1-NE2
4.32
1.36
1.32
1
1
C
416
HIS
CE1-NE2
4.32
1.36
1.32
1
1
A
219
HIS
CE1-NE2
4.31
1.36
1.32
1
1
C
114
HIS
CE1-NE2
4.31
1.36
1.32
1
1
B
9
HIS
CE1-NE2
4.31
1.36
1.32
1
1
A
219
HIS
CD2-NE2
4.30
1.33
1.37
1
1
C
117
HIS
CE1-NE2
4.30
1.36
1.32
1
1
B
32
HIS
CE1-NE2
4.30
1.36
1.32
1
1
C
394
HIS
CD2-NE2
4.30
1.33
1.37
1
1
A
111
HIS
CD2-NE2
4.29
1.33
1.37
1
1
B
25
HIS
CE1-NE2
4.29
1.36
1.32
1
1
A
210
HIS
CE1-NE2
4.29
1.36
1.32
1
1
C
197
HIS
CD2-NE2
4.29
1.33
1.37
1
1
A
30
HIS
CD2-NE2
4.28
1.33
1.37
1
1
C
476
HIS
CD2-NE2
4.28
1.33
1.37
1
1
C
281
HIS
CD2-NE2
4.28
1.33
1.37
1
1
C
134
HIS
CD2-NE2
4.28
1.33
1.37
1
1
C
199
HIS
CD2-NE2
4.27
1.33
1.37
1
1
A
30
HIS
CE1-NE2
4.27
1.36
1.32
1
1
C
16
HIS
CD2-NE2
4.27
1.33
1.37
1
1
C
114
HIS
CD2-NE2
4.26
1.33
1.37
1
1
B
25
HIS
CD2-NE2
4.26
1.33
1.37
1
1
A
159
HIS
CE1-NE2
4.26
1.36
1.32
1
1
C
190
HIS
CE1-NE2
4.26
1.36
1.32
1
1
A
295
HIS
CD2-NE2
4.25
1.33
1.37
1
1
C
16
HIS
CE1-NE2
4.25
1.36
1.32
1
1
C
88
HIS
CE1-NE2
4.24
1.36
1.32
1
1
A
295
HIS
CE1-NE2
4.24
1.36
1.32
1
1
B
9
HIS
CD2-NE2
4.24
1.33
1.37
1
1
A
198
HIS
CD2-NE2
4.24
1.33
1.37
1
1
C
190
HIS
CD2-NE2
4.24
1.33
1.37
1
1
A
353
HIS
CE1-NE2
4.24
1.36
1.32
1
1
A
210
HIS
CD2-NE2
4.23
1.33
1.37
1
1
C
117
HIS
CD2-NE2
4.23
1.33
1.37
1
1
C
88
HIS
CD2-NE2
4.21
1.33
1.37
1
1
C
134
HIS
CE1-NE2
4.21
1.36
1.32
1
1
C
416
HIS
CD2-NE2
4.21
1.33
1.37
1
1
A
159
HIS
CD2-NE2
4.21
1.33
1.37
1
1
C
281
HIS
CE1-NE2
4.19
1.36
1.32
1
1
B
32
HIS
CD2-NE2
4.16
1.33
1.37
1
1

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
1.68
24

There are 24 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)
C:459:ARG:O
C:460:LYS:C
0.69
1
1
C:436:CYS:O
C:437:ASN:C
0.65
1
1
C:436:CYS:O
C:437:ASN:O
0.63
1
1
C:62:TYR:N
C:63:PRO:HD2
0.60
1
1
A:42:LEU:C
A:42:LEU:HD13
0.57
1
1
C:71:ALA:N
C:72:PRO:CD
0.57
1
1
A:327:LEU:O
A:328:VAL:HG13
0.55
1
1
C:339:VAL:N
C:340:PRO:CD
0.54
1
1
C:365:GLU:O
C:366:THR:CB
0.53
1
1
C:305:LEU:N
C:306:PRO:CD
0.52
1
1
C:369:GLY:O
C:370:ARG:CB
0.51
1
1
C:455:LEU:O
C:456:ASP:C
0.51
1
1
A:203:LEU:N
A:203:LEU:HD12
0.48
1
1
C:62:TYR:N
C:63:PRO:CD
0.48
1
1
A:15:ASN:OD1
A:16:GLY:N
0.48
1
1
C:165:TYR:C
C:165:TYR:CD1
0.47
1
1
C:365:GLU:O
C:366:THR:HB
0.47
1
1
A:87:PHE:HA
A:88:PRO:C
0.46
1
1
C:501:THR:OG1
C:502:THR:N
0.43
1
1
C:388:MET:N
C:389:PRO:CD
0.42
1
1
C:467:SEP:O
C:468:TYR:C
0.42
1
1
C:62:TYR:HB3
C:63:PRO:HD3
0.42
1
1
C:165:TYR:CD1
C:166:THR:N
0.41
1
1
A:15:ASN:C
A:15:ASN:OD1
0.41
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
874
811
50
13

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

Chain Res Type Models (Total)
A
6
THR
1
A
159
HIS
1
A
328
VAL
1
A
333
GLY
1
C
149
THR
1
C
331
GLY
1
C
366
THR
1
C
370
ARG
1
C
374
ARG
1
C
437
ASN
1
C
459
ARG
1
C
460
LYS
1
C
482
VAL
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
766
714
39
13

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

Chain Res Type Models (Total)
A
30
HIS
1
A
40
VAL
1
A
50
GLU
1
A
204
ASP
1
A
327
LEU
1
A
328
VAL
1
A
329
VAL
1
A
335
LEU
1
A
338
LEU
1
C
268
THR
1
C
370
ARG
1
C
373
THR
1
C
495
ARG
1