SMTL ID : 6mrm.3 (3 other biounits)

Red Clover Necrotic Mosaic Virus

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-18-mer

Ligands

18 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: D.127, D.130 Chain B: D.97, D.169, Q.211 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.127, A:D.130, A:D.130, B:D.97, B:D.97 CA.2: 5 residues within 4Å: Chain A: D.97, D.169, Q.211 Chain C: D.127, D.130 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain A Metal complexes: C:D.127, C:D.130, C:D.130, A:D.97, A:D.169 CA.3: 4 residues within 4Å: Chain B: D.127, D.130 Chain C: D.97, Q.211 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Metal complexes: C:D.97, B:D.127, B:D.130, B:D.130 CA.4: 5 residues within 4Å: Chain D: D.127, D.130 Chain E: D.97, D.169, Q.211 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Metal complexes: D:D.127, D:D.130, D:D.130, E:D.97, E:D.97 CA.5: 5 residues within 4Å: Chain D: D.97, D.169, Q.211 Chain F: D.127, D.130 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain F Metal complexes: D:D.97, D:D.169, F:D.127, F:D.130, F:D.130 CA.6: 4 residues within 4Å: Chain E: D.127, D.130 Chain F: D.97, Q.211 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain E Metal complexes: F:D.97, E:D.127, E:D.130, E:D.130 CA.7: 5 residues within 4Å: Chain G: D.127, D.130 Chain H: D.97, D.169, Q.211 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain H Metal complexes: G:D.127, G:D.130, G:D.130, H:D.97, H:D.97 CA.8: 5 residues within 4Å: Chain G: D.97, D.169, Q.211 Chain I: D.127, D.130 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain I Metal complexes: G:D.97, G:D.169, I:D.127, I:D.130, I:D.130 CA.9: 4 residues within 4Å: Chain H: D.127, D.130 Chain I: D.97, Q.211 4 PLIP interactions: 3 interactions with chain H, 1 interactions with chain I Metal complexes: H:D.127, H:D.130, H:D.130, I:D.97 CA.10: 5 residues within 4Å: Chain J: D.127, D.130 Chain K: D.97, D.169, Q.211 5 PLIP interactions: 3 interactions with chain J, 2 interactions with chain K Metal complexes: J:D.127, J:D.130, J:D.130, K:D.97, K:D.97 CA.11: 5 residues within 4Å: Chain J: D.97, D.169, Q.211 Chain L: D.127, D.130 5 PLIP interactions: 2 interactions with chain J, 3 interactions with chain L Metal complexes: J:D.97, J:D.169, L:D.127, L:D.130, L:D.130 CA.12: 4 residues within 4Å: Chain K: D.127, D.130 Chain L: D.97, Q.211 4 PLIP interactions: 1 interactions with chain L, 3 interactions with chain K Metal complexes: L:D.97, K:D.127, K:D.130, K:D.130 CA.13: 5 residues within 4Å: Chain M: D.127, D.130 Chain N: D.97, D.169, Q.211 5 PLIP interactions: 3 interactions with chain M, 2 interactions with chain N Metal complexes: M:D.127, M:D.130, M:D.130, N:D.97, N:D.97 CA.14: 5 residues within 4Å: Chain M: D.97, D.169, Q.211 Chain O: D.127, D.130 5 PLIP interactions: 2 interactions with chain M, 3 interactions with chain O Metal complexes: M:D.97, M:D.169, O:D.127, O:D.130, O:D.130 CA.15: 4 residues within 4Å: Chain N: D.127, D.130 Chain O: D.97, Q.211 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain O Metal complexes: N:D.127, N:D.130, N:D.130, O:D.97 CA.16: 5 residues within 4Å: Chain P: D.127, D.130 Chain Q: D.97, D.169, Q.211 5 PLIP interactions: 3 interactions with chain P, 2 interactions with chain Q Metal complexes: P:D.127, P:D.130, P:D.130, Q:D.97, Q:D.97 CA.17: 5 residues within 4Å: Chain P: D.97, D.169, Q.211 Chain R: D.127, D.130 5 PLIP interactions: 2 interactions with chain P, 3 interactions with chain R Metal complexes: P:D.97, P:D.169, R:D.127, R:D.130, R:D.130 CA.18: 4 residues within 4Å: Chain Q: D.127, D.130 Chain R: D.97, Q.211 4 PLIP interactions: 3 interactions with chain Q, 1 interactions with chain R Metal complexes: Q:D.127, Q:D.130, Q:D.130, R:D.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sherman, M.B. et al., Near-Atomic-Resolution Cryo-Electron Microscopy Structures of Cucumber Leaf Spot Virus and Red Clover Necrotic Mosaic Virus: Evolutionary Divergence at the Icosahedral Three-Fold Axes. J.Virol. (2020)

Release Date

2019-10-16

Peptides

Capsid protein: ABCDEFGHIJKLMNOPQR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

G
A

H
B

I
C

J
A

K
B

L
C

M
A

N
B

O
C

P
A

Q
B

R
C

Capsid protein

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