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SMTL ID : 5cpx.1
Crystal structure of murine polyomavirus PTA strain VP1 in complex with the DSLNT glycan
Coordinates
PDB Format
Method
X-RAY DIFFRACTION 1.87 Å
Oligo State
homo-pentamer
Ligands
3 x
NAG
-
GAL
-
SIA
:
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
NAG-GAL-SIA.1:
10 residues within 4Å:
Chain A:
Y.40
,
R.45
,
G.46
,
E.59
,
N.61
,
T.62
,
T.259
,
N.261
,
H.266
Chain B:
D.53
11
PLIP interactions
:
11 interactions with chain A
Hydrogen bonds:
A:N.61
,
A:N.61
,
A:Y.40
,
A:Y.40
,
A:R.45
,
A:G.46
,
A:H.266
Water bridges:
A:I.47
,
A:E.59
,
A:Q.39
,
A:N.261
,
A:N.261
,
A:N.261
Salt bridges:
A:R.45
,
A:H.266
NAG-GAL-SIA.4:
10 residues within 4Å:
Chain D:
Y.40
,
R.45
,
G.46
,
E.59
,
N.61
,
T.62
,
T.259
,
N.261
,
H.266
Chain E:
D.53
10
PLIP interactions
:
10 interactions with chain D
Hydrogen bonds:
D:N.61
,
D:N.61
,
D:Y.40
,
D:R.45
,
D:G.46
,
D:H.266
Water bridges:
D:I.47
,
D:Y.40
,
D:Y.40
,
D:N.261
,
D:N.261
Salt bridges:
D:R.45
,
D:H.266
NAG-GAL-SIA.5:
10 residues within 4Å:
Chain A:
D.53
Chain E:
Y.40
,
R.45
,
G.46
,
E.59
,
N.61
,
T.62
,
T.259
,
N.261
,
H.266
9
PLIP interactions
:
8 interactions with chain E
,
1 interactions with chain A
Hydrogen bonds:
E:N.61
,
E:N.61
,
E:Y.40
,
E:Y.40
,
E:R.45
,
E:G.46
,
E:N.261
,
E:H.266
Water bridges:
E:I.47
,
E:E.59
Salt bridges:
E:R.45
,
E:H.266
Hydrophobic interactions:
A:D.53
2 x
GAL
-
SIA
:
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose
(Non-covalent)
GAL-SIA.2:
10 residues within 4Å:
Chain B:
Y.40
,
R.45
,
G.46
,
E.59
,
N.61
,
T.62
,
T.259
,
N.261
,
H.266
Chain C:
D.53
11
PLIP interactions
:
10 interactions with chain B
,
1 interactions with chain C
Hydrogen bonds:
B:N.61
,
B:N.61
,
B:Y.40
,
B:Y.40
,
B:R.45
,
B:G.46
,
B:N.261
,
B:H.266
Water bridges:
B:I.47
,
B:Q.39
,
B:R.257
Salt bridges:
B:R.45
,
B:H.266
Hydrophobic interactions:
C:D.53
GAL-SIA.3:
10 residues within 4Å:
Chain C:
Y.40
,
R.45
,
G.46
,
E.59
,
N.61
,
T.62
,
T.259
,
N.261
,
H.266
Chain D:
D.53
12
PLIP interactions
:
11 interactions with chain C
,
1 interactions with chain D
Hydrogen bonds:
C:G.46
,
C:N.61
,
C:N.61
,
C:Y.40
,
C:R.45
,
C:G.46
,
C:H.266
Hydrophobic interactions:
D:D.53
Water bridges:
C:Y.40
,
C:Y.40
,
C:N.261
,
C:N.261
,
C:N.261
Salt bridges:
C:R.45
,
C:H.266
4 x
GOL
:
GLYCEROL
(Non-functional Binders)
GOL.6:
8 residues within 4Å:
Chain A:
E.203
,
N.204
,
R.206
,
D.233
,
V.237
,
G.238
,
P.239
,
L.240
6
PLIP interactions
:
6 interactions with chain A
Hydrogen bonds:
A:N.204
,
A:R.206
,
A:R.206
,
A:D.233
,
A:D.233
,
A:L.240
GOL.7:
3 residues within 4Å:
Chain B:
K.154
,
E.155
,
E.156
3
PLIP interactions
:
3 interactions with chain B
Hydrogen bonds:
B:E.155
,
B:E.156
,
B:E.156
GOL.8:
3 residues within 4Å:
Chain D:
K.154
,
E.155
,
E.156
3
PLIP interactions
:
3 interactions with chain D
Hydrogen bonds:
D:E.155
,
D:E.156
Water bridges:
D:E.156
GOL.9:
8 residues within 4Å:
Chain E:
E.203
,
N.204
,
R.206
,
D.233
,
V.237
,
G.238
,
P.239
,
L.240
5
PLIP interactions
:
5 interactions with chain E
Hydrogen bonds:
E:N.204
,
E:R.206
,
E:R.206
,
E:D.233
,
E:L.240
Links
RCSB
PDBe
PDBe-KB
PDBj
PDBsum
CATH
PLIP
Citation
Buch, M.H. et al., Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity. Plos Pathog. (2015)
Release Date
2015-10-28
Peptides
VP1:
A
B
C
D
E
SMTL:PDB
SMTL Chain Id:
PDB Chain Id:
A
A
B
B
C
C
D
D
E
E
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VP1
Toggle Identical (ACE)
Related Entries With Identical Sequence
5cpu.1
|
5cpw.1
|
5cpy.1
Cartoon
Cartoon
Tube
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Lines
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Licorice
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