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
478
SEP
O3P-P
4.83
1.51
1.61
1
1
C
493
SEP
O2P-P
4.83
1.51
1.61
1
1
C
467
SEP
O3P-P
4.83
1.51
1.61
1
1
C
463
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
467
SEP
O1P-P
4.81
1.51
1.61
1
1
C
478
SEP
O1P-P
4.80
1.51
1.61
1
1
C
467
SEP
O2P-P
4.80
1.51
1.61
1
1
C
493
SEP
O3P-P
4.79
1.51
1.61
1
1
C
478
SEP
O2P-P
4.78
1.51
1.61
1
1
C
463
SEP
O2P-P
4.78
1.51
1.61
1
1
C
463
SEP
O3P-P
4.77
1.51
1.61
1
1
C
463
SEP
OG-P
4.39
1.52
1.61
1
1
C
467
SEP
OG-P
4.38
1.52
1.61
1
1
C
416
HIS
CE1-NE2
4.38
1.36
1.32
1
1
C
478
SEP
OG-P
4.37
1.52
1.61
1
1
A
111
HIS
CE1-NE2
4.36
1.36
1.32
1
1
A
219
HIS
CE1-NE2
4.35
1.36
1.32
1
1
C
493
SEP
OG-P
4.35
1.52
1.61
1
1
A
159
HIS
CD2-NE2
4.34
1.33
1.37
1
1
A
295
HIS
CD2-NE2
4.34
1.33
1.37
1
1
A
210
HIS
CE1-NE2
4.32
1.36
1.32
1
1
A
159
HIS
CE1-NE2
4.32
1.36
1.32
1
1
C
88
HIS
CE1-NE2
4.32
1.36
1.32
1
1
C
117
HIS
CE1-NE2
4.32
1.36
1.32
1
1
B
32
HIS
CE1-NE2
4.31
1.36
1.32
1
1
A
353
HIS
CE1-NE2
4.31
1.36
1.32
1
1
C
199
HIS
CE1-NE2
4.31
1.36
1.32
1
1
C
114
HIS
CD2-NE2
4.30
1.33
1.37
1
1
C
16
HIS
CD2-NE2
4.30
1.33
1.37
1
1
C
114
HIS
CE1-NE2
4.30
1.36
1.32
1
1
C
199
HIS
CD2-NE2
4.30
1.33
1.37
1
1
C
281
HIS
CE1-NE2
4.30
1.36
1.32
1
1
B
9
HIS
CE1-NE2
4.30
1.36
1.32
1
1
A
111
HIS
CD2-NE2
4.30
1.33
1.37
1
1
C
16
HIS
CE1-NE2
4.29
1.36
1.32
1
1
C
394
HIS
CE1-NE2
4.29
1.36
1.32
1
1
A
198
HIS
CE1-NE2
4.29
1.36
1.32
1
1
C
281
HIS
CD2-NE2
4.29
1.33
1.37
1
1
C
416
HIS
CD2-NE2
4.29
1.33
1.37
1
1
B
32
HIS
CD2-NE2
4.29
1.33
1.37
1
1
C
134
HIS
CE1-NE2
4.28
1.36
1.32
1
1
C
197
HIS
CE1-NE2
4.28
1.36
1.32
1
1
A
30
HIS
CD2-NE2
4.27
1.33
1.37
1
1
C
476
HIS
CE1-NE2
4.27
1.36
1.32
1
1
C
197
HIS
CD2-NE2
4.26
1.33
1.37
1
1
A
30
HIS
CE1-NE2
4.26
1.36
1.32
1
1
C
88
HIS
CD2-NE2
4.26
1.33
1.37
1
1
A
219
HIS
CD2-NE2
4.26
1.33
1.37
1
1
C
190
HIS
CE1-NE2
4.26
1.36
1.32
1
1
A
210
HIS
CD2-NE2
4.25
1.33
1.37
1
1
A
198
HIS
CD2-NE2
4.25
1.33
1.37
1
1
A
353
HIS
CD2-NE2
4.24
1.33
1.37
1
1
B
9
HIS
CD2-NE2
4.24
1.33
1.37
1
1
C
134
HIS
CD2-NE2
4.24
1.33
1.37
1
1
C
476
HIS
CD2-NE2
4.23
1.33
1.37
1
1
C
117
HIS
CD2-NE2
4.23
1.33
1.37
1
1
B
25
HIS
CE1-NE2
4.22
1.36
1.32
1
1
C
394
HIS
CD2-NE2
4.22
1.33
1.37
1
1
B
25
HIS
CD2-NE2
4.22
1.33
1.37
1
1
C
190
HIS
CD2-NE2
4.22
1.33
1.37
1
1
A
295
HIS
CE1-NE2
4.21
1.36
1.32
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
1.54
22

There are 22 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:165:TYR:C
C:165:TYR:CD1
0.67
1
1
C:165:TYR:CD1
C:166:THR:N
0.60
1
1
C:71:ALA:N
C:72:PRO:CD
0.58
1
1
C:62:TYR:N
C:63:PRO:HD2
0.57
1
1
A:224:THR:OG1
A:225:ASN:N
0.54
1
1
C:339:VAL:N
C:340:PRO:CD
0.53
1
1
C:305:LEU:N
C:306:PRO:CD
0.52
1
1
A:243:LEU:C
A:243:LEU:HD23
0.51
1
1
A:87:PHE:HA
A:88:PRO:C
0.49
1
1
C:62:TYR:HB3
C:63:PRO:HD3
0.49
1
1
A:203:LEU:HD22
A:349:PHE:CE1
0.48
1
1
C:321:ALA:O
C:322:ASN:C
0.46
1
1
C:388:MET:HB2
C:389:PRO:HD3
0.46
1
1
C:62:TYR:N
C:63:PRO:CD
0.45
1
1
C:123:ASP:C
C:123:ASP:OD1
0.45
1
1
C:1:ASP:C
C:1:ASP:OD1
0.44
1
1
C:490:LEU:HA
C:491:PRO:C
0.44
1
1
A:95:LYS:N
A:96:PRO:HD2
0.42
1
1
C:47:SER:O
C:48:THR:C
0.42
1
1
C:388:MET:N
C:389:PRO:CD
0.42
1
1
C:70:GLU:O
C:73:THR:HG22
0.41
1
1
C:466:SER:OG
C:467:SEP:N
0.40
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
820
45
9

There are 9 unique backbone outliers. Detailed list of outliers are tabulated below.

Chain Res Type Models (Total)
C
149
THR
1
C
322
ASN
1
C
331
GLY
1
C
370
ARG
1
C
459
ARG
1
C
465
SER
1
C
470
TYR
1
C
483
GLY
1
C
485
ARG
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
719
35
12

There are 12 unique sidechain outliers. Detailed list of outliers are tabulated below.

Chain Res Type Models (Total)
A
6
THR
1
A
18
LEU
1
A
26
ASP
1
A
58
THR
1
A
79
LEU
1
A
143
ASP
1
A
156
GLU
1
A
214
ILE
1
A
335
LEU
1
A
353
HIS
1
C
373
THR
1
C
479
VAL
1