SMTL ID : 7x01.1

Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with inhibitor FHA

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.79, E.129, C.134, C.141 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.79, A:E.129, A:E.129, A:C.134, A:C.141 ZN.3: 4 residues within 4Å: Chain B: H.79, E.129, C.134, C.141 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.79, B:E.129, B:E.129, B:C.134, B:C.141 ZN.5: 4 residues within 4Å: Chain C: H.79, E.129, C.134, C.141 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.79, C:E.129, C:E.129, C:C.134, C:C.141 ZN.7: 4 residues within 4Å: Chain D: H.79, E.129, C.134, C.141 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.79, D:E.129, D:E.129, D:C.134, D:C.141 ZN.9: 4 residues within 4Å: Chain E: H.79, E.129, C.134, C.141 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:H.79, E:E.129, E:E.129, E:C.134, E:C.141 ZN.11: 4 residues within 4Å: Chain F: H.79, E.129, C.134, C.141 5 PLIP interactions: 5 interactions with chain F Metal complexes: F:H.79, F:E.129, F:E.129, F:C.134, F:C.141 ZN.13: 4 residues within 4Å: Chain G: H.79, E.129, C.134, C.141 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:H.79, G:E.129, G:E.129, G:C.134, G:C.141 ZN.15: 4 residues within 4Å: Chain H: H.79, E.129, C.134, C.141 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:H.79, H:E.129, H:E.129, H:C.134, H:C.141 ZN.17: 4 residues within 4Å: Chain I: H.79, E.129, C.134, C.141 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:H.79, I:E.129, I:E.129, I:C.134, I:C.141 ZN.19: 4 residues within 4Å: Chain J: H.79, E.129, C.134, C.141 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:H.79, J:E.129, J:E.129, J:C.134, J:C.141 ZN.21: 4 residues within 4Å: Chain K: H.79, E.129, C.134, C.141 5 PLIP interactions: 5 interactions with chain K Metal complexes: K:H.79, K:E.129, K:E.129, K:C.134, K:C.141 ZN.23: 4 residues within 4Å: Chain L: H.79, E.129, C.134, C.141 5 PLIP interactions: 5 interactions with chain L Metal complexes: L:H.79, L:E.129, L:E.129, L:C.134, L:C.141

12 x 7XQ: (1R,2S,3S,4R,5R)-3-(6-aminopurin-9-yl)-4-fluoranyl-5-(2-hydroxyethyl)cyclopentane-1,2-diol(Non-covalent)

7XQ.2: 9 residues within 4Å: Chain A: I.64, G.65, P.83, E.88, D.89, T.137, D.138, Q.151, D.152 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.86, A:S.86, A:D.138, A:D.138, A:Q.151 7XQ.4: 9 residues within 4Å: Chain B: I.64, G.65, P.83, E.88, D.89, T.137, D.138, Q.151, D.152 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.65, B:D.89, B:D.138, B:D.138, B:Q.151 7XQ.6: 9 residues within 4Å: Chain C: I.64, G.65, P.83, E.88, D.89, T.137, D.138, Q.151, D.152 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.65, C:D.89, C:D.138, C:D.138, C:Q.151 7XQ.8: 9 residues within 4Å: Chain D: I.64, G.65, P.83, E.88, D.89, T.137, D.138, Q.151, D.152 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.65, D:S.86, D:S.86, D:D.138, D:D.138, D:Q.151 7XQ.10: 10 residues within 4Å: Chain E: I.64, G.65, P.83, R.85, E.88, D.89, T.137, D.138, Q.151, D.152 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.65, E:S.86, E:D.89, E:D.138, E:D.138, E:Q.151 7XQ.12: 10 residues within 4Å: Chain F: I.64, G.65, P.83, R.85, E.88, D.89, T.137, D.138, Q.151, D.152 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:G.65, F:D.89, F:D.138, F:D.138, F:Q.151 7XQ.14: 9 residues within 4Å: Chain G: I.64, G.65, P.83, E.88, D.89, T.137, D.138, Q.151, D.152 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:S.86, G:S.86, G:D.138, G:D.138, G:Q.151 7XQ.16: 9 residues within 4Å: Chain H: I.64, G.65, P.83, E.88, D.89, T.137, D.138, Q.151, D.152 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:G.65, H:D.89, H:D.138, H:D.138, H:Q.151 7XQ.18: 9 residues within 4Å: Chain I: I.64, G.65, P.83, E.88, D.89, T.137, D.138, Q.151, D.152 5 PLIP interactions: 5 interactions with chain I Hydrogen bonds: I:G.65, I:D.89, I:D.138, I:D.138, I:Q.151 7XQ.20: 9 residues within 4Å: Chain J: I.64, G.65, P.83, E.88, D.89, T.137, D.138, Q.151, D.152 5 PLIP interactions: 5 interactions with chain J Hydrogen bonds: J:G.65, J:D.89, J:D.138, J:D.138, J:Q.151 7XQ.22: 9 residues within 4Å: Chain K: I.64, G.65, P.83, E.88, D.89, T.137, D.138, Q.151, D.152 5 PLIP interactions: 5 interactions with chain K Hydrogen bonds: K:G.65, K:D.89, K:D.138, K:D.138, K:Q.151 7XQ.24: 9 residues within 4Å: Chain L: I.64, G.65, P.83, E.88, D.89, T.137, D.138, Q.151, D.152 5 PLIP interactions: 5 interactions with chain L Hydrogen bonds: L:G.65, L:D.89, L:D.138, L:D.138, L:Q.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, K. et al., Molecular basis of specific viral RNA recognition and 5'-end capping by the Chikungunya virus nsP1. Cell Rep (2022)

Release Date

2022-08-10

Peptides

mRNA-capping enzyme nsP1: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

mRNA-capping enzyme nsP1

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