SMTL ID : 8axv.1

Structure of an open form of CHIKV nsP1 capping pores

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.79, E.129, C.134, C.141, R.142, Q.143 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.79, A:E.129, A:C.141 ZN.3: 6 residues within 4Å: Chain B: H.79, E.129, C.134, C.141, R.142, Q.143 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.79, B:E.129, B:C.141 ZN.5: 6 residues within 4Å: Chain C: H.79, E.129, C.134, C.141, R.142, Q.143 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.79, C:E.129, C:C.141 ZN.7: 6 residues within 4Å: Chain D: H.79, E.129, C.134, C.141, R.142, Q.143 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.79, D:E.129, D:C.141 ZN.9: 6 residues within 4Å: Chain E: H.79, E.129, C.134, C.141, R.142, Q.143 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.79, E:E.129, E:C.141 ZN.11: 6 residues within 4Å: Chain F: H.79, E.129, C.134, C.141, R.142, Q.143 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.79, F:E.129, F:C.141 ZN.13: 6 residues within 4Å: Chain G: H.79, E.129, C.134, C.141, R.142, Q.143 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:H.79, G:E.129, G:C.141 ZN.15: 6 residues within 4Å: Chain H: H.79, E.129, C.134, C.141, R.142, Q.143 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:H.79, H:E.129, H:C.141 ZN.17: 6 residues within 4Å: Chain I: H.79, E.129, C.134, C.141, R.142, Q.143 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:H.79, I:E.129, I:C.141 ZN.19: 6 residues within 4Å: Chain J: H.79, E.129, C.134, C.141, R.142, Q.143 3 PLIP interactions: 3 interactions with chain J Metal complexes: J:H.79, J:E.129, J:C.141 ZN.21: 6 residues within 4Å: Chain K: H.79, E.129, C.134, C.141, R.142, Q.143 3 PLIP interactions: 3 interactions with chain K Metal complexes: K:H.79, K:E.129, K:C.141 ZN.23: 6 residues within 4Å: Chain L: H.79, E.129, C.134, C.141, R.142, Q.143 3 PLIP interactions: 3 interactions with chain L Metal complexes: L:H.79, L:E.129, L:C.141

12 x MY6: 2-amino-7-methyl-1,7-dihydro-6H-purin-6-one(Covalent)

MY6.2: 5 residues within 4Å: Chain A: D.152, Y.154, F.241, Y.248, E.250 5 PLIP interactions: 5 interactions with chain A Salt bridges: A:D.152, A:E.250 pi-Stacking: A:Y.248, A:Y.248 pi-Cation interactions: A:Y.248 MY6.4: 5 residues within 4Å: Chain B: D.152, Y.154, F.241, Y.248, E.250 5 PLIP interactions: 5 interactions with chain B Salt bridges: B:D.152, B:E.250 pi-Stacking: B:Y.248, B:Y.248 pi-Cation interactions: B:Y.248 MY6.6: 5 residues within 4Å: Chain C: D.152, Y.154, F.241, Y.248, E.250 5 PLIP interactions: 5 interactions with chain C Salt bridges: C:D.152, C:E.250 pi-Stacking: C:Y.248, C:Y.248 pi-Cation interactions: C:Y.248 MY6.8: 5 residues within 4Å: Chain D: D.152, Y.154, F.241, Y.248, E.250 5 PLIP interactions: 5 interactions with chain D Salt bridges: D:D.152, D:E.250 pi-Stacking: D:Y.248, D:Y.248 pi-Cation interactions: D:Y.248 MY6.10: 5 residues within 4Å: Chain E: D.152, Y.154, F.241, Y.248, E.250 5 PLIP interactions: 5 interactions with chain E Salt bridges: E:D.152, E:E.250 pi-Stacking: E:Y.248, E:Y.248 pi-Cation interactions: E:Y.248 MY6.12: 5 residues within 4Å: Chain F: D.152, Y.154, F.241, Y.248, E.250 5 PLIP interactions: 5 interactions with chain F Salt bridges: F:D.152, F:E.250 pi-Stacking: F:Y.248, F:Y.248 pi-Cation interactions: F:Y.248 MY6.14: 5 residues within 4Å: Chain G: D.152, Y.154, F.241, Y.248, E.250 5 PLIP interactions: 5 interactions with chain G Salt bridges: G:D.152, G:E.250 pi-Stacking: G:Y.248, G:Y.248 pi-Cation interactions: G:Y.248 MY6.16: 5 residues within 4Å: Chain H: D.152, Y.154, F.241, Y.248, E.250 5 PLIP interactions: 5 interactions with chain H Salt bridges: H:D.152, H:E.250 pi-Stacking: H:Y.248, H:Y.248 pi-Cation interactions: H:Y.248 MY6.18: 5 residues within 4Å: Chain I: D.152, Y.154, F.241, Y.248, E.250 5 PLIP interactions: 5 interactions with chain I Salt bridges: I:D.152, I:E.250 pi-Stacking: I:Y.248, I:Y.248 pi-Cation interactions: I:Y.248 MY6.20: 5 residues within 4Å: Chain J: D.152, Y.154, F.241, Y.248, E.250 5 PLIP interactions: 5 interactions with chain J Salt bridges: J:D.152, J:E.250 pi-Stacking: J:Y.248, J:Y.248 pi-Cation interactions: J:Y.248 MY6.22: 5 residues within 4Å: Chain K: D.152, Y.154, F.241, Y.248, E.250 5 PLIP interactions: 5 interactions with chain K Salt bridges: K:D.152, K:E.250 pi-Stacking: K:Y.248, K:Y.248 pi-Cation interactions: K:Y.248 MY6.24: 5 residues within 4Å: Chain L: D.152, Y.154, F.241, Y.248, E.250 5 PLIP interactions: 5 interactions with chain L Salt bridges: L:D.152, L:E.250 pi-Stacking: L:Y.248, L:Y.248 pi-Cation interactions: L:Y.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jones, R. et al., Structural basis and dynamics of Chikungunya alphavirus RNA capping by nsP1 capping pores. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-03-29

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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