SMTL ID : 4llf.1 (2 other biounits)

Crystal structure of Cucumber Necrosis Virus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

homo-15-mer

Ligands

15 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.173, D.175, D.178 Chain B: D.145, Q.258 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.145 CA.2: 5 residues within 4Å: Chain B: D.173, D.175, D.178 Chain C: D.145, Q.258 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Metal complexes: B:D.173, C:D.145 CA.4: 5 residues within 4Å: Chain A: D.145, Q.258 Chain C: D.173, D.175, D.178 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C Metal complexes: A:D.145, C:D.173, C:D.178 CA.5: 5 residues within 4Å: Chain D: D.145, Q.258 Chain F: D.173, D.175, D.178 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Metal complexes: D:D.145, F:D.178 CA.6: 5 residues within 4Å: Chain D: D.173, D.175, D.178 Chain E: D.145, Q.258 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.173, D:D.178 CA.7: 5 residues within 4Å: Chain E: D.173, D.175, D.178 Chain F: D.145, Q.258 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:D.145 CA.9: 5 residues within 4Å: Chain G: D.145, Q.258 Chain I: D.173, D.175, D.178 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain G Metal complexes: I:D.173, I:D.178, G:D.145 CA.10: 5 residues within 4Å: Chain G: D.173, D.175, D.178 Chain H: D.145, Q.258 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:D.145 CA.11: 5 residues within 4Å: Chain H: D.173, D.175, D.178 Chain I: D.145, Q.258 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain I Metal complexes: H:D.175, I:D.145 CA.13: 4 residues within 4Å: Chain J: D.145, Q.258 Chain L: D.173, D.178 2 PLIP interactions: 1 interactions with chain L, 1 interactions with chain J Metal complexes: L:D.178, J:D.145 CA.14: 5 residues within 4Å: Chain J: D.173, D.175, D.178 Chain K: D.145, Q.258 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain J Metal complexes: K:D.145, J:D.178 CA.16: 5 residues within 4Å: Chain K: D.173, D.175, D.178 Chain L: D.145, Q.258 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain L Metal complexes: K:D.173, L:D.145 CA.17: 4 residues within 4Å: Chain M: D.145, Q.258 Chain O: D.173, D.178 3 PLIP interactions: 1 interactions with chain M, 2 interactions with chain O Metal complexes: M:D.145, O:D.173, O:D.178 CA.18: 5 residues within 4Å: Chain N: D.173, D.175, D.178 Chain O: D.145, Q.258 3 PLIP interactions: 1 interactions with chain N, 2 interactions with chain O Metal complexes: N:D.173, O:D.145, O:D.145 CA.19: 5 residues within 4Å: Chain M: D.173, D.175, D.178 Chain N: D.145, Q.258 1 PLIP interactions: 1 interactions with chain M Metal complexes: M:D.178

5 x ZN: ZINC ION(Non-covalent)

ZN.3: 1 residues within 4Å: Chain C: H.62 No protein-ligand interaction detected (PLIP) ZN.8: 1 residues within 4Å: Chain F: H.62 No protein-ligand interaction detected (PLIP) ZN.12: 1 residues within 4Å: Chain I: H.62 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:H.62 ZN.15: 1 residues within 4Å: Chain L: H.62 No protein-ligand interaction detected (PLIP) ZN.20: 1 residues within 4Å: Chain O: H.62 1 PLIP interactions: 1 interactions with chain O Metal complexes: O:H.62

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, M. et al., Atomic structure of cucumber necrosis virus and the role of the capsid in vector transmission. J.Virol. (2013)

Release Date

2013-10-30

Peptides

Capsid protein: ABCDEFGHIJKLMNO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
D

D
E

E
F

F
G

G
H

H
I

I
J

J
K

K
L

L
M

M
N

N
O

O
P

Capsid protein

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