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 98 bond length outliers in this entry (1.05% of 9302 assessed bonds). A summary is provided below.

Chain Res Type Atoms |Z| Observed (Å) Ideal (Å) Model ID (Worst) Models (Total)
D
58
ASP
C-N
27.77
0.94
1.33
1
1
A
58
ASP
C-N
27.75
0.94
1.33
1
1
E
76
ALA
C-N
17.05
1.09
1.33
1
1
F
76
ALA
C-N
17.02
1.09
1.33
1
1
D
63
ASP
C-N
15.47
1.11
1.33
1
1
A
63
ASP
C-N
15.45
1.11
1.33
1
1
A
54
SER
C-N
15.04
1.12
1.33
1
1
D
54
SER
C-N
14.98
1.12
1.33
1
1
A
67
ALA
C-N
14.61
1.12
1.33
1
1
D
67
ALA
C-N
14.57
1.13
1.33
1
1
A
62
ALA
C-N
14.10
1.13
1.33
1
1
D
62
ALA
C-N
14.03
1.13
1.33
1
1
D
71
GLU
C-N
12.59
1.15
1.33
1
1
A
71
GLU
C-N
12.54
1.15
1.33
1
1
A
70
GLU
C-N
12.32
1.16
1.33
1
1
D
70
GLU
C-N
12.29
1.16
1.33
1
1
F
55
MET
C-N
12.26
1.50
1.33
1
1
A
34
ARG
C-N
11.71
1.17
1.33
1
1
D
34
ARG
C-N
11.64
1.17
1.33
1
1
A
66
ARG
C-N
10.73
1.18
1.33
1
1
D
66
ARG
C-N
10.66
1.18
1.33
1
1
D
44
LEU
C-N
10.53
1.48
1.33
1
1
A
44
LEU
C-N
10.52
1.48
1.33
1
1
E
61
VAL
C-N
10.38
1.18
1.33
1
1
F
61
VAL
C-N
10.36
1.18
1.33
1
1
A
39
SER
C-N
10.28
1.19
1.33
1
1
D
65
GLU
C-N
10.24
1.19
1.33
1
1
A
65
GLU
C-N
10.19
1.19
1.33
1
1
D
52
TRP
C-N
10.18
1.19
1.33
1
1
D
39
SER
C-N
10.14
1.19
1.33
1
1
A
52
TRP
C-N
10.14
1.19
1.33
1
1
A
57
GLU
C-N
9.65
1.46
1.33
1
1
D
57
GLU
C-N
9.63
1.46
1.33
1
1
A
74
ALA
C-N
8.99
1.20
1.33
1
1
D
74
ALA
C-N
8.98
1.20
1.33
1
1
D
53
SER
C-N
8.84
1.21
1.33
1
1
A
53
SER
C-N
8.84
1.21
1.33
1
1
F
37
GLU
C-N
8.74
1.45
1.33
1
1
E
37
GLU
C-N
8.70
1.45
1.33
1
1
F
67
ALA
C-N
8.29
1.21
1.33
1
1
E
67
ALA
C-N
8.29
1.21
1.33
1
1
F
65
GLU
C-N
7.97
1.22
1.33
1
1
E
65
GLU
C-N
7.96
1.22
1.33
1
1
D
37
GLU
C-N
7.78
1.22
1.33
1
1
A
37
GLU
C-N
7.77
1.22
1.33
1
1
E
64
MET
C-N
7.65
1.22
1.33
1
1
F
64
MET
C-N
7.63
1.22
1.33
1
1
E
47
LYS
C-N
7.62
1.22
1.33
1
1
F
47
LYS
C-N
7.61
1.22
1.33
1
1
E
58
ASP
C-N
7.40
1.23
1.33
1
1
F
58
ASP
C-N
7.38
1.23
1.33
1
1
F
44
LEU
C-N
6.86
1.42
1.33
1
1
E
44
LEU
C-N
6.81
1.42
1.33
1
1
F
33
LYS
C-N
6.69
1.42
1.33
1
1
E
33
LYS
C-N
6.63
1.42
1.33
1
1
E
73
ALA
C-N
6.61
1.42
1.33
1
1
F
73
ALA
C-N
6.53
1.42
1.33
1
1
E
75
ALA
C-N
6.49
1.42
1.33
1
1
F
75
ALA
C-N
6.45
1.42
1.33
1
1
A
33
LYS
C-N
6.45
1.24
1.33
1
1
D
46
GLN
C-N
6.37
1.42
1.33
1
1
D
33
LYS
C-N
6.36
1.24
1.33
1
1
E
68
GLN
C-N
6.29
1.24
1.33
1
1
F
68
GLN
C-N
6.29
1.24
1.33
1
1
F
48
TRP
C-N
6.27
1.42
1.33
1
1
A
46
GLN
C-N
6.26
1.42
1.33
1
1
E
48
TRP
C-N
6.20
1.42
1.33
1
1
D
69
LEU
C-N
6.20
1.24
1.33
1
1
A
69
LEU
C-N
6.15
1.24
1.33
1
1
D
68
GLN
C-N
5.93
1.25
1.33
1
1
A
68
GLN
C-N
5.90
1.25
1.33
1
1
D
47
LYS
C-N
5.90
1.25
1.33
1
1
A
47
LYS
C-N
5.88
1.25
1.33
1
1
F
30
LEU
C-N
5.86
1.41
1.33
1
1
A
59
ALA
C-N
5.81
1.25
1.33
1
1
E
63
ASP
C-N
5.78
1.25
1.33
1
1
F
63
ASP
C-N
5.76
1.25
1.33
1
1
D
59
ALA
C-N
5.74
1.25
1.33
1
1
E
30
LEU
C-N
5.71
1.41
1.33
1
1
A
64
MET
C-N
5.63
1.25
1.33
1
1
D
64
MET
C-N
5.53
1.25
1.33
1
1
D
56
SER
C-N
5.44
1.41
1.33
1
1
A
56
SER
C-N
5.39
1.40
1.33
1
1
D
76
ALA
C-N
5.27
1.26
1.33
1
1
A
76
ALA
C-N
5.25
1.26
1.33
1
1
E
74
ALA
C-N
5.22
1.40
1.33
1
1
F
74
ALA
C-N
5.20
1.40
1.33
1
1
A
35
LEU
C-N
5.08
1.40
1.33
1
1
D
35
LEU
C-N
5.07
1.40
1.33
1
1
E
57
GLU
C-N
4.72
1.26
1.33
1
1
F
57
GLU
C-N
4.66
1.26
1.33
1
1
E
34
ARG
C-N
4.61
1.39
1.33
1
1
F
34
ARG
C-N
4.59
1.39
1.33
1
1
E
60
SER
C-N
4.52
1.27
1.33
1
1
F
60
SER
C-N
4.48
1.27
1.33
1
1
D
51
MET
C-N
4.23
1.27
1.33
1
1
A
51
MET
C-N
4.19
1.27
1.33
1
1
D
31
LEU
C-N
4.03
1.27
1.33
1
1

Standard geometry: angle outliers ?

There are 136 bond angle outliers in this entry (1.09% of 12494 assessed bonds). A summary is provided below. The output is limited to 100 rows.

Chain Res Type Atoms |Z| Observed (Å) Ideal (Å) Model ID (Worst) Models (Total)
F
55
MET
O-C-N
48.86
44.82
123.00
1
1
F
55
MET
CA-C-N
23.48
163.17
116.20
1
1
C
51
SER
CA-C-O
14.25
163.74
121.00
1
1
C
51
SER
CA-C-OXT
12.83
82.52
121.00
1
1
C
51
SER
O-C-OXT
12.25
81.24
118.00
1
1
D
56
SER
O-C-N
11.85
104.04
123.00
1
1
A
56
SER
O-C-N
11.83
104.06
123.00
1
1
A
54
SER
O-C-N
11.10
105.25
123.00
1
1
D
54
SER
O-C-N
11.07
105.28
123.00
1
1
D
59
ALA
O-C-N
10.56
106.10
123.00
1
1
A
59
ALA
O-C-N
10.55
106.12
123.00
1
1
A
30
LEU
C-N-CA
9.91
139.54
121.70
1
1
D
30
LEU
C-N-CA
9.90
139.51
121.70
1
1
D
55
MET
O-C-N
9.41
107.95
123.00
1
1
A
55
MET
O-C-N
9.38
107.99
123.00
1
1
A
57
GLU
C-N-CA
9.04
137.97
121.70
1
1
D
57
GLU
C-N-CA
9.00
137.89
121.70
1
1
A
56
SER
CA-C-N
8.89
133.98
116.20
1
1
D
56
SER
CA-C-N
8.88
133.96
116.20
1
1
E
73
ALA
O-C-N
8.82
137.11
123.00
1
1
F
73
ALA
O-C-N
8.79
137.06
123.00
1
1
A
58
ASP
O-C-N
8.27
109.78
123.00
1
1
D
58
ASP
O-C-N
8.26
109.78
123.00
1
1
A
43
GLN
C-N-CA
8.00
107.30
121.70
1
1
D
43
GLN
C-N-CA
7.96
107.37
121.70
1
1
E
73
ALA
C-N-CA
7.79
107.68
121.70
1
1
F
73
ALA
C-N-CA
7.76
107.73
121.70
1
1
D
53
SER
O-C-N
7.59
110.86
123.00
1
1
A
53
SER
O-C-N
7.58
110.87
123.00
1
1
D
52
TRP
O-C-N
7.45
111.07
123.00
1
1
A
52
TRP
O-C-N
7.45
111.08
123.00
1
1
D
55
MET
CA-C-N
7.27
130.74
116.20
1
1
A
55
MET
CA-C-N
7.26
130.72
116.20
1
1
E
73
ALA
CA-C-N
7.10
101.99
116.20
1
1
F
73
ALA
CA-C-N
7.10
102.00
116.20
1
1
A
57
GLU
O-C-N
6.97
111.85
123.00
1
1
D
57
GLU
O-C-N
6.92
111.93
123.00
1
1
A
54
SER
CA-C-N
6.78
129.75
116.20
1
1
D
54
SER
CA-C-N
6.75
129.71
116.20
1
1
A
76
ALA
C-N-CA
6.25
110.46
121.70
1
1
A
37
GLU
CA-C-N
6.24
103.72
116.20
1
1
D
37
GLU
CA-C-N
6.24
103.72
116.20
1
1
D
76
ALA
C-N-CA
6.24
110.47
121.70
1
1
F
55
MET
C-N-CA
6.23
132.91
121.70
1
1
E
63
ASP
C-N-CA
6.11
110.69
121.70
1
1
F
63
ASP
C-N-CA
6.09
110.74
121.70
1
1
A
33
LYS
C-N-CA
6.08
132.65
121.70
1
1
D
33
LYS
C-N-CA
6.08
132.64
121.70
1
1
D
58
ASP
CA-C-N
6.02
128.25
116.20
1
1
A
58
ASP
CA-C-N
6.00
128.20
116.20
1
1
D
37
GLU
O-C-N
6.00
132.60
123.00
1
1
A
37
GLU
O-C-N
6.00
132.59
123.00
1
1
D
59
ALA
CA-C-N
5.92
128.04
116.20
1
1
A
59
ALA
CA-C-N
5.92
128.04
116.20
1
1
D
38
ASP
C-N-CA
5.88
111.11
121.70
1
1
A
38
ASP
C-N-CA
5.85
111.17
121.70
1
1
A
52
TRP
CA-C-N
5.70
127.60
116.20
1
1
D
52
TRP
CA-C-N
5.69
127.57
116.20
1
1
A
62
ALA
O-C-N
5.48
114.23
123.00
1
1
D
62
ALA
O-C-N
5.48
114.23
123.00
1
1
H
49
GLN
OE1-CD-NE2
5.47
117.13
122.60
1
1
E
55
MET
C-N-CA
5.44
111.91
121.70
1
1
D
76
ALA
O-C-N
5.43
114.31
123.00
1
1
A
76
ALA
O-C-N
5.40
114.37
123.00
1
1
E
70
GLU
O-C-N
5.34
131.54
123.00
1
1
F
70
GLU
O-C-N
5.33
131.53
123.00
1
1
D
60
SER
O-C-N
5.21
114.66
123.00
1
1
F
63
ASP
O-C-N
5.20
131.32
123.00
1
1
A
60
SER
O-C-N
5.20
114.68
123.00
1
1
E
63
ASP
O-C-N
5.19
131.31
123.00
1
1
D
40
SER
O-C-N
5.15
131.24
123.00
1
1
A
53
SER
CA-C-N
5.15
126.49
116.20
1
1
D
53
SER
CA-C-N
5.14
126.47
116.20
1
1
E
66
ARG
C-N-CA
5.12
112.48
121.70
1
1
F
66
ARG
C-N-CA
5.09
112.55
121.70
1
1
F
70
GLU
C-N-CA
5.08
112.56
121.70
1
1
A
40
SER
O-C-N
5.07
131.11
123.00
1
1
E
70
GLU
C-N-CA
5.07
112.58
121.70
1
1
A
68
GLN
C-N-CA
5.04
112.63
121.70
1
1
D
68
GLN
C-N-CA
5.03
112.65
121.70
1
1
G
188
GLN
OE1-CD-NE2
4.98
117.62
122.60
1
1
D
52
TRP
C-N-CA
4.97
130.65
121.70
1
1
A
52
TRP
C-N-CA
4.96
130.64
121.70
1
1
C
49
GLN
OE1-CD-NE2
4.90
117.70
122.60
1
1
C
129
GLN
OE1-CD-NE2
4.86
117.74
122.60
1
1
C
127
GLN
OE1-CD-NE2
4.78
117.82
122.60
1
1
D
56
SER
C-N-CA
4.76
130.28
121.70
1
1
F
30
LEU
C-N-CA
4.75
130.25
121.70
1
1
E
30
LEU
C-N-CA
4.75
130.25
121.70
1
1
A
56
SER
C-N-CA
4.74
130.23
121.70
1
1
H
129
GLN
OE1-CD-NE2
4.73
117.87
122.60
1
1
A
35
LEU
C-N-CA
4.70
113.23
121.70
1
1
E
66
ARG
O-C-N
4.69
130.51
123.00
1
1
H
127
GLN
OE1-CD-NE2
4.69
117.91
122.60
1
1
D
35
LEU
C-N-CA
4.67
113.29
121.70
1
1
F
66
ARG
O-C-N
4.65
130.44
123.00
1
1
D
40
SER
CA-C-N
4.61
106.97
116.20
1
1
G
71
GLN
OE1-CD-NE2
4.58
118.02
122.60
1
1
A
40
SER
CA-C-N
4.57
107.05
116.20
1
1
A
38
ASP
CA-C-N
4.52
107.17
116.20
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
49.39
905

There are 905 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)
D:215:LEU:HD21
F:52:TRP:CZ3
1.69
1
1
E:48:TRP:CE2
E:211:VAL:HG13
1.65
1
1
D:193:PHE:CD2
F:44:LEU:HB2
1.64
1
1
E:191:GLU:HB3
G:105:VAL:CG1
1.63
1
1
F:51:MET:HE3
F:211:VAL:CA
1.62
1
1
B:95:TRP:CE3
F:198:ARG:CD
1.61
1
1
A:211:VAL:HG13
E:48:TRP:CH2
1.60
1
1
B:95:TRP:CZ3
F:198:ARG:CD
1.59
1
1
F:59:ALA:HB1
F:203:LYS:CG
1.58
1
1
D:215:LEU:CD2
F:52:TRP:CH2
1.58
1
1
D:215:LEU:CD2
F:52:TRP:CZ3
1.57
1
1
B:105:VAL:CG1
F:191:GLU:HB3
1.56
1
1
E:77:GLU:HG3
G:162:PHE:CZ
1.56
1
1
D:211:VAL:CG2
F:48:TRP:CZ3
1.55
1
1
E:191:GLU:CD
G:105:VAL:HG21
1.55
1
1
E:77:GLU:CG
G:162:PHE:CZ
1.55
1
1
B:105:VAL:HG21
F:191:GLU:CD
1.53
1
1
F:59:ALA:CB
F:203:LYS:HG3
1.52
1
1
E:62:ALA:CB
E:203:LYS:HD2
1.51
1
1
A:48:TRP:HH2
G:214:MET:SD
1.51
1
1
F:51:MET:CE
F:211:VAL:HA
1.51
1
1
E:62:ALA:HB3
E:203:LYS:CD
1.49
1
1
E:191:GLU:CG
G:163:CYS:SG
1.47
1
1
D:215:LEU:HD23
F:52:TRP:CH2
1.47
1
1
A:211:VAL:CG1
E:48:TRP:CH2
1.46
1
1
E:191:GLU:HG3
G:163:CYS:SG
1.45
1
1
E:48:TRP:NE1
E:211:VAL:HG13
1.45
1
1
A:48:TRP:CH2
G:214:MET:SD
1.43
1
1
B:105:VAL:CG2
F:191:GLU:CD
1.43
1
1
B:95:TRP:CD2
F:198:ARG:HD3
1.42
1
1
D:211:VAL:HG22
F:48:TRP:CZ3
1.42
1
1
B:163:CYS:SG
F:191:GLU:CG
1.41
1
1
F:48:TRP:CE2
F:211:VAL:CG1
1.41
1
1
B:163:CYS:SG
F:191:GLU:HG3
1.41
1
1
F:48:TRP:NE1
F:211:VAL:HG13
1.40
1
1
E:191:GLU:CD
G:105:VAL:CG2
1.40
1
1
D:77:GLU:OE2
D:79:ARG:CD
1.40
1
1
B:95:TRP:CE3
F:198:ARG:HD3
1.40
1
1
B:95:TRP:CZ3
F:198:ARG:HD3
1.39
1
1
E:48:TRP:CZ2
E:211:VAL:CG1
1.39
1
1
F:54:SER:CA
F:57:GLU:HB3
1.39
1
1
D:193:PHE:CD2
F:44:LEU:CB
1.39
1
1
F:59:ALA:CB
F:203:LYS:CG
1.37
1
1
F:59:ALA:O
F:63:ASP:HB2
1.36
1
1
D:194:ASN:CB
F:37:GLU:HB3
1.34
1
1
F:48:TRP:CE2
F:211:VAL:HG13
1.34
1
1
D:207:GLN:OE1
F:41:ARG:NH1
1.33
1
1
E:54:SER:O
E:58:ASP:N
1.33
1
1
E:77:GLU:HG3
G:162:PHE:CE1
1.32
1
1
E:52:TRP:CE3
E:211:VAL:HG21
1.31
1
1
D:193:PHE:HE2
F:44:LEU:C
1.31
1
1
D:193:PHE:CE2
F:45:LEU:N
1.31
1
1
E:48:TRP:CE2
E:211:VAL:CG1
1.31
1
1
F:51:MET:CE
F:211:VAL:CA
1.30
1
1
F:55:MET:CA
F:58:ASP:HB2
1.30
1
1
E:62:ALA:N
E:203:LYS:HZ2
1.30
1
1
A:38:ASP:O
A:42:HIS:ND1
1.30
1
1
E:63:ASP:H
E:203:LYS:NZ
1.29
1
1
E:191:GLU:HA
G:158:LEU:CD2
1.29
1
1
E:53:SER:O
E:57:GLU:N
1.29
1
1
F:48:TRP:NE1
F:211:VAL:CG1
1.29
1
1
F:51:MET:HE3
F:211:VAL:N
1.29
1
1
E:59:ALA:O
E:63:ASP:HB2
1.28
1
1
B:95:TRP:CE3
F:198:ARG:HD2
1.28
1
1
B:158:LEU:CD2
F:191:GLU:HA
1.28
1
1
D:193:PHE:HE2
F:45:LEU:N
1.27
1
1
F:56:SER:O
F:203:LYS:HE3
1.26
1
1
B:105:VAL:CG1
F:191:GLU:CB
1.26
1
1
A:52:TRP:CH2
G:218:SER:OG
1.26
1
1
D:194:ASN:ND2
F:38:ASP:N
1.25
1
1
E:191:GLU:OE1
G:105:VAL:CG2
1.25
1
1
B:95:TRP:CH2
F:198:ARG:HD3
1.25
1
1
D:38:ASP:O
D:42:HIS:ND1
1.24
1
1
A:211:VAL:CG1
E:48:TRP:CZ2
1.24
1
1
B:95:TRP:CE2
F:198:ARG:HD3
1.24
1
1
F:54:SER:HA
F:57:GLU:CB
1.22
1
1
A:36:SER:O
A:39:SER:OG
1.21
1
1
D:36:SER:O
D:39:SER:OG
1.21
1
1
D:194:ASN:HD21
F:38:ASP:CA
1.20
1
1
D:38:ASP:HB3
D:42:HIS:CE1
1.20
1
1
A:38:ASP:HB3
A:42:HIS:CE1
1.20
1
1
B:105:VAL:CG2
F:191:GLU:OE1
1.20
1
1
E:191:GLU:CG
G:158:LEU:HD13
1.19
1
1
A:38:ASP:O
A:70:GLU:OE2
1.19
1
1
A:211:VAL:HG13
E:48:TRP:CZ2
1.18
1
1
D:38:ASP:O
D:70:GLU:OE2
1.18
1
1
E:191:GLU:CB
G:105:VAL:CG1
1.18
1
1
B:158:LEU:HD13
F:191:GLU:CG
1.17
1
1
D:53:SER:CB
D:59:ALA:O
1.17
1
1
D:194:ASN:HD21
F:38:ASP:N
1.17
1
1
E:57:GLU:HA
E:60:SER:HB3
1.17
1
1
B:95:TRP:CZ2
F:198:ARG:HD3
1.17
1
1
A:53:SER:CB
A:59:ALA:O
1.16
1
1
E:59:ALA:CB
E:207:GLN:NE2
1.16
1
1
A:215:LEU:HD23
E:52:TRP:HH2
1.16
1
1
E:191:GLU:CA
G:158:LEU:HD22
1.16
1
1
E:59:ALA:HB3
E:207:GLN:HE22
1.14
1
1
B:95:TRP:CH2
F:198:ARG:CD
1.14
1
1
F:57:GLU:HA
F:60:SER:HB3
1.14
1
1
B:97:LEU:HD12
F:191:GLU:OE2
1.14
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
1132
1094
31
7

There are 7 unique backbone outliers. Detailed list of outliers are tabulated below.

Chain Res Type Models (Total)
A
57
GLU
1
B
191
PRO
1
C
21
ARG
1
D
57
GLU
1
F
56
SER
1
G
191
PRO
1
H
21
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
1038
956
61
21

There are 21 unique sidechain outliers. Detailed list of outliers are tabulated below.

Chain Res Type Models (Total)
A
30
LEU
1
A
38
ASP
1
B
101
LEU
1
B
201
GLU
1
B
214
MET
1
B
218
SER
1
C
24
LEU
1
D
30
LEU
1
D
38
ASP
1
E
30
LEU
1
E
56
SER
1
E
64
MET
1
F
30
LEU
1
F
56
SER
1
F
64
MET
1
G
101
LEU
1
G
187
ILE
1
G
201
GLU
1
G
214
MET
1
G
218
SER
1
H
24
LEU
1