SMTL ID : 7d6n.1

Crystal structure of tick-borne encephalitis virus RNA-dependent RNA polymerase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.17 Å

Oligo State

homo-10-mer

Ligands

20 x ZN: ZINC ION(Non-covalent)

ZN.1: 3 residues within 4Å: Chain A: H.452, C.466, C.585 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.452, A:C.466, A:C.585 ZN.2: 4 residues within 4Å: Chain A: E.176, H.180, C.185, C.188 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.176, A:H.180, A:C.185, A:C.188 ZN.4: 3 residues within 4Å: Chain B: H.452, C.466, C.585 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.452, B:C.466, B:C.585 ZN.5: 4 residues within 4Å: Chain B: E.176, H.180, C.185, C.188 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.176, B:H.180, B:C.185, B:C.188 ZN.7: 3 residues within 4Å: Chain C: H.452, C.466, C.585 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.452, C:C.466, C:C.585 ZN.8: 6 residues within 4Å: Chain C: E.176, H.180, C.185, A.186, H.187, C.188 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:E.176, C:E.176, C:H.180, C:C.185, C:C.188 ZN.10: 3 residues within 4Å: Chain D: H.452, C.466, C.585 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:C.466, D:C.585 ZN.11: 4 residues within 4Å: Chain D: E.176, H.180, C.185, C.188 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.176, D:H.180, D:C.185, D:C.188 ZN.13: 3 residues within 4Å: Chain E: H.452, C.466, C.585 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.452, E:C.466, E:C.585 ZN.14: 6 residues within 4Å: Chain E: E.176, H.180, C.185, A.186, H.187, C.188 5 PLIP interactions: 5 interactions with chain E Metal complexes: E:E.176, E:E.176, E:H.180, E:C.185, E:C.188 ZN.16: 3 residues within 4Å: Chain F: H.452, C.466, C.585 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.452, F:C.466, F:C.585 ZN.17: 4 residues within 4Å: Chain F: E.176, H.180, C.185, C.188 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:E.176, F:H.180, F:C.185, F:C.188 ZN.19: 3 residues within 4Å: Chain G: H.452, C.466, C.585 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.452, G:C.466, G:C.585 ZN.20: 4 residues within 4Å: Chain G: E.176, H.180, C.185, C.188 5 PLIP interactions: 5 interactions with chain G Metal complexes: G:E.176, G:E.176, G:H.180, G:C.185, G:C.188 ZN.22: 3 residues within 4Å: Chain H: H.452, C.466, C.585 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:H.452, H:C.466, H:C.585 ZN.23: 5 residues within 4Å: Chain H: E.176, H.180, C.185, A.186, C.188 5 PLIP interactions: 5 interactions with chain H Metal complexes: H:E.176, H:E.176, H:H.180, H:C.185, H:C.188 ZN.25: 3 residues within 4Å: Chain I: H.452, C.466, C.585 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:H.452, I:C.466, I:C.585 ZN.26: 6 residues within 4Å: Chain I: E.176, H.180, C.185, A.186, H.187, C.188 5 PLIP interactions: 5 interactions with chain I Metal complexes: I:E.176, I:E.176, I:H.180, I:C.185, I:C.188 ZN.28: 3 residues within 4Å: Chain J: H.452, C.466, C.585 2 PLIP interactions: 2 interactions with chain J Metal complexes: J:C.466, J:C.585 ZN.29: 4 residues within 4Å: Chain J: E.176, H.180, C.185, C.188 5 PLIP interactions: 5 interactions with chain J Metal complexes: J:E.176, J:E.176, J:H.180, J:C.185, J:C.188

10 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: A.270, D.272, D.402, C.403, P.445 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.272, A:D.402 MG.6: 6 residues within 4Å: Chain B: A.270, D.271, D.272, D.402, C.403, P.445 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.272, B:D.402 MG.9: 5 residues within 4Å: Chain C: A.270, D.272, D.402, C.403, P.445 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.272, C:D.402 MG.12: 5 residues within 4Å: Chain D: A.270, D.272, D.402, C.403, P.445 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.272, D:D.272, D:D.402 MG.15: 5 residues within 4Å: Chain E: A.270, D.272, D.402, C.403, P.445 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.272, E:D.272, E:D.402 MG.18: 5 residues within 4Å: Chain F: A.270, D.272, D.402, C.403, P.445 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.272, F:D.402 MG.21: 5 residues within 4Å: Chain G: A.270, D.272, D.402, C.403, P.445 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:D.272, G:D.272, G:D.402 MG.24: 5 residues within 4Å: Chain H: A.270, D.272, D.402, C.403, P.445 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:D.272, H:D.272, H:D.402 MG.27: 5 residues within 4Å: Chain I: A.270, D.272, D.402, C.403, P.445 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:D.272, I:D.402 MG.30: 5 residues within 4Å: Chain J: A.270, D.272, D.402, C.403, P.445 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:D.272, J:D.272, J:D.402, J:D.402

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, J. et al., Crystal structure of tick-borne encephalitis virus. Nucleic Acids Res. (2020)

Release Date

2020-12-23

Peptides

Tick-borne encephalitis virus RNA-dependent RNA polymerase: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
E

D
D

E
C

F
F

G
G

H
J

I
I

J
H

Tick-borne encephalitis virus RNA-dependent RNA polymerase