SMTL ID : 4nwv.3 (4 other biounits)

Crystal structure of Orsay virus-like particle

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

homo-18-mer

Ligands

18 x CA: CALCIUM ION(Non-covalent)

CA.1: 4 residues within 4Å: Chain A: Q.92, E.166 Chain B: D.122, D.125 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.122, B:D.125 CA.2: 4 residues within 4Å: Chain A: D.122, D.125 Chain C: Q.92, E.166 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.122, A:D.125 CA.3: 5 residues within 4Å: Chain B: Q.92, E.166 Chain C: D.122, D.125, R.176 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.166 CA.4: 4 residues within 4Å: Chain D: Q.92, E.166 Chain E: D.122, D.125 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.122, E:D.125 CA.5: 4 residues within 4Å: Chain D: D.122, D.125 Chain F: Q.92, E.166 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.122, D:D.125 CA.6: 5 residues within 4Å: Chain E: Q.92, E.166 Chain F: D.122, D.125, R.176 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.166 CA.7: 4 residues within 4Å: Chain G: Q.92, E.166 Chain H: D.122, D.125 2 PLIP interactions: 2 interactions with chain H Metal complexes: H:D.122, H:D.125 CA.8: 4 residues within 4Å: Chain G: D.122, D.125 Chain I: Q.92, E.166 2 PLIP interactions: 2 interactions with chain G Metal complexes: G:D.122, G:D.125 CA.9: 5 residues within 4Å: Chain H: Q.92, E.166 Chain I: D.122, D.125, R.176 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.166 CA.10: 4 residues within 4Å: Chain J: Q.92, E.166 Chain K: D.122, D.125 2 PLIP interactions: 2 interactions with chain K Metal complexes: K:D.122, K:D.125 CA.11: 4 residues within 4Å: Chain J: D.122, D.125 Chain L: Q.92, E.166 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:D.122, J:D.125 CA.12: 5 residues within 4Å: Chain K: Q.92, E.166 Chain L: D.122, D.125, R.176 1 PLIP interactions: 1 interactions with chain K Metal complexes: K:E.166 CA.13: 4 residues within 4Å: Chain M: Q.92, E.166 Chain N: D.122, D.125 2 PLIP interactions: 2 interactions with chain N Metal complexes: N:D.122, N:D.125 CA.14: 4 residues within 4Å: Chain M: D.122, D.125 Chain O: Q.92, E.166 2 PLIP interactions: 2 interactions with chain M Metal complexes: M:D.122, M:D.125 CA.15: 5 residues within 4Å: Chain N: Q.92, E.166 Chain O: D.122, D.125, R.176 1 PLIP interactions: 1 interactions with chain N Metal complexes: N:E.166 CA.16: 4 residues within 4Å: Chain P: Q.92, E.166 Chain Q: D.122, D.125 2 PLIP interactions: 2 interactions with chain Q Metal complexes: Q:D.122, Q:D.125 CA.17: 4 residues within 4Å: Chain P: D.122, D.125 Chain R: Q.92, E.166 2 PLIP interactions: 2 interactions with chain P Metal complexes: P:D.122, P:D.125 CA.18: 5 residues within 4Å: Chain Q: Q.92, E.166 Chain R: D.122, D.125, R.176 1 PLIP interactions: 1 interactions with chain Q Metal complexes: Q:E.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, Y.R. et al., Crystal structure of a nematode-infecting virus. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-08-20

Peptides

Capsid protein: ABCDEFGHIJKLMNOPQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
B

D
A

E
C

F
B

G
A

H
C

I
B

J
A

K
C

L
B

M
A

N
C

O
B

P
A

Q
C

R
B

Capsid protein

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