SMTL ID : 7fgg.1

Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7GTP

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 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.79, A:E.129, A:C.134, A:C.141 ZN.5: 4 residues within 4Å: Chain B: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.79, B:E.129, B:C.134, B:C.141 ZN.9: 4 residues within 4Å: Chain C: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.79, C:E.129, C:C.134, C:C.141 ZN.13: 4 residues within 4Å: Chain D: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.79, D:E.129, D:C.134, D:C.141 ZN.17: 4 residues within 4Å: Chain E: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.79, E:E.129, E:C.134, E:C.141 ZN.21: 4 residues within 4Å: Chain F: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.79, F:E.129, F:C.134, F:C.141 ZN.25: 4 residues within 4Å: Chain G: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.79, G:E.129, G:C.134, G:C.141 ZN.29: 4 residues within 4Å: Chain H: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.79, H:E.129, H:C.134, H:C.141 ZN.33: 4 residues within 4Å: Chain I: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain I Metal complexes: I:H.79, I:E.129, I:C.134, I:C.141 ZN.37: 4 residues within 4Å: Chain J: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain J Metal complexes: J:H.79, J:E.129, J:C.134, J:C.141 ZN.41: 4 residues within 4Å: Chain K: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain K Metal complexes: K:H.79, K:E.129, K:C.134, K:C.141 ZN.45: 4 residues within 4Å: Chain L: H.79, E.129, C.134, C.141 4 PLIP interactions: 4 interactions with chain L Metal complexes: L:H.79, L:E.129, L:C.134, L:C.141

12 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 11 residues within 4Å: Chain A: G.65, R.70, P.83, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.85, A:D.89, A:R.92, A:D.138, A:D.138, A:Q.151, A:Q.151 Water bridges: A:R.41, A:R.41, A:A.67, A:A.67, A:R.70, A:D.89, A:D.89, A:Q.151, A:D.152 Salt bridges: A:R.70 SAH.6: 11 residues within 4Å: Chain B: G.65, R.70, P.83, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.7 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.85, B:D.89, B:R.92, B:D.138, B:D.138, B:Q.151, B:Q.151 Water bridges: B:R.41, B:R.41, B:A.67, B:A.67, B:R.70, B:D.89, B:D.89, B:Q.151, B:D.152 Salt bridges: B:R.70 SAH.10: 11 residues within 4Å: Chain C: G.65, R.70, P.83, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.11 17 PLIP interactions: 17 interactions with chain C Hydrogen bonds: C:R.85, C:D.89, C:R.92, C:D.138, C:D.138, C:Q.151, C:Q.151 Water bridges: C:R.41, C:R.41, C:A.67, C:A.67, C:R.70, C:D.89, C:D.89, C:Q.151, C:D.152 Salt bridges: C:R.70 SAH.14: 11 residues within 4Å: Chain D: G.65, R.70, P.83, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.15 17 PLIP interactions: 17 interactions with chain D Hydrogen bonds: D:R.85, D:D.89, D:R.92, D:D.138, D:D.138, D:Q.151, D:Q.151 Water bridges: D:R.41, D:R.41, D:A.67, D:A.67, D:R.70, D:D.89, D:D.89, D:Q.151, D:D.152 Salt bridges: D:R.70 SAH.18: 11 residues within 4Å: Chain E: G.65, R.70, P.83, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.19 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:R.85, E:D.89, E:R.92, E:D.138, E:D.138, E:Q.151, E:Q.151 Water bridges: E:R.41, E:R.41, E:A.67, E:A.67, E:R.70, E:D.89, E:D.89, E:Q.151, E:D.152 Salt bridges: E:R.70 SAH.22: 11 residues within 4Å: Chain F: G.65, R.70, P.83, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.23 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:R.85, F:D.89, F:R.92, F:D.138, F:D.138, F:Q.151, F:Q.151 Water bridges: F:R.41, F:R.41, F:A.67, F:A.67, F:R.70, F:D.89, F:D.89, F:Q.151, F:D.152 Salt bridges: F:R.70 SAH.26: 11 residues within 4Å: Chain G: G.65, R.70, P.83, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.27 17 PLIP interactions: 17 interactions with chain G Hydrogen bonds: G:R.85, G:D.89, G:R.92, G:D.138, G:D.138, G:Q.151, G:Q.151 Water bridges: G:R.41, G:R.41, G:A.67, G:A.67, G:R.70, G:D.89, G:D.89, G:Q.151, G:D.152 Salt bridges: G:R.70 SAH.30: 11 residues within 4Å: Chain H: G.65, R.70, P.83, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.31 17 PLIP interactions: 17 interactions with chain H Hydrogen bonds: H:R.85, H:D.89, H:R.92, H:D.138, H:D.138, H:Q.151, H:Q.151 Water bridges: H:R.41, H:R.41, H:A.67, H:A.67, H:R.70, H:D.89, H:D.89, H:Q.151, H:D.152 Salt bridges: H:R.70 SAH.34: 11 residues within 4Å: Chain I: G.65, R.70, P.83, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.35 17 PLIP interactions: 17 interactions with chain I Hydrogen bonds: I:R.85, I:D.89, I:R.92, I:D.138, I:D.138, I:Q.151, I:Q.151 Water bridges: I:R.41, I:R.41, I:A.67, I:A.67, I:R.70, I:D.89, I:D.89, I:Q.151, I:D.152 Salt bridges: I:R.70 SAH.38: 11 residues within 4Å: Chain J: G.65, R.70, P.83, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.39 17 PLIP interactions: 17 interactions with chain J Hydrogen bonds: J:R.85, J:D.89, J:R.92, J:D.138, J:D.138, J:Q.151, J:Q.151 Water bridges: J:R.41, J:R.41, J:A.67, J:A.67, J:R.70, J:D.89, J:D.89, J:Q.151, J:D.152 Salt bridges: J:R.70 SAH.42: 11 residues within 4Å: Chain K: G.65, R.70, P.83, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.43 17 PLIP interactions: 17 interactions with chain K Hydrogen bonds: K:R.85, K:D.89, K:R.92, K:D.138, K:D.138, K:Q.151, K:Q.151 Water bridges: K:R.41, K:R.41, K:A.67, K:A.67, K:R.70, K:D.89, K:D.89, K:Q.151, K:D.152 Salt bridges: K:R.70 SAH.46: 11 residues within 4Å: Chain L: G.65, R.70, P.83, R.85, D.89, R.92, T.137, D.138, Q.151, V.156 Ligands: MGP.47 17 PLIP interactions: 17 interactions with chain L Hydrogen bonds: L:R.85, L:D.89, L:R.92, L:D.138, L:D.138, L:Q.151, L:Q.151 Water bridges: L:R.41, L:R.41, L:A.67, L:A.67, L:R.70, L:D.89, L:D.89, L:Q.151, L:D.152 Salt bridges: L:R.70

12 x MGP: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

MGP.3: 14 residues within 4Å: Chain A: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285 Ligands: SAH.2, MG.4 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:R.41, A:R.70, A:R.92, A:Y.285 Water bridges: A:N.35, A:N.35, A:A.40, A:R.41, A:R.41, A:D.152 Salt bridges: A:H.37, A:R.41, A:R.41, A:R.70, A:E.250 pi-Stacking: A:Y.248 MGP.7: 14 residues within 4Å: Chain B: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285 Ligands: SAH.6, MG.8 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.41, B:R.70, B:R.92, B:Y.285 Water bridges: B:N.35, B:N.35, B:A.40, B:R.41, B:R.41, B:D.152 Salt bridges: B:H.37, B:R.41, B:R.41, B:R.70, B:E.250 pi-Stacking: B:Y.248 MGP.11: 14 residues within 4Å: Chain C: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285 Ligands: SAH.10, MG.12 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:R.41, C:R.70, C:R.92, C:Y.285 Water bridges: C:N.35, C:N.35, C:A.40, C:R.41, C:R.41, C:D.152 Salt bridges: C:H.37, C:R.41, C:R.41, C:R.70, C:E.250 pi-Stacking: C:Y.248 MGP.15: 14 residues within 4Å: Chain D: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285 Ligands: SAH.14, MG.16 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:R.41, D:R.70, D:R.92, D:Y.285 Water bridges: D:N.35, D:N.35, D:A.40, D:R.41, D:R.41, D:D.152 Salt bridges: D:H.37, D:R.41, D:R.41, D:R.70, D:E.250 pi-Stacking: D:Y.248 MGP.19: 14 residues within 4Å: Chain E: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285 Ligands: SAH.18, MG.20 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:R.41, E:R.70, E:R.92, E:Y.285 Water bridges: E:N.35, E:N.35, E:A.40, E:R.41, E:R.41, E:D.152 Salt bridges: E:H.37, E:R.41, E:R.41, E:R.70, E:E.250 pi-Stacking: E:Y.248 MGP.23: 14 residues within 4Å: Chain F: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285 Ligands: SAH.22, MG.24 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:R.41, F:R.70, F:R.92, F:Y.285 Water bridges: F:N.35, F:N.35, F:A.40, F:R.41, F:R.41, F:D.152 Salt bridges: F:H.37, F:R.41, F:R.41, F:R.70, F:E.250 pi-Stacking: F:Y.248 MGP.27: 14 residues within 4Å: Chain G: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285 Ligands: SAH.26, MG.28 16 PLIP interactions: 16 interactions with chain G Hydrogen bonds: G:R.41, G:R.70, G:R.92, G:Y.285 Water bridges: G:N.35, G:N.35, G:A.40, G:R.41, G:R.41, G:D.152 Salt bridges: G:H.37, G:R.41, G:R.41, G:R.70, G:E.250 pi-Stacking: G:Y.248 MGP.31: 14 residues within 4Å: Chain H: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285 Ligands: SAH.30, MG.32 16 PLIP interactions: 16 interactions with chain H Hydrogen bonds: H:R.41, H:R.70, H:R.92, H:Y.285 Water bridges: H:N.35, H:N.35, H:A.40, H:R.41, H:R.41, H:D.152 Salt bridges: H:H.37, H:R.41, H:R.41, H:R.70, H:E.250 pi-Stacking: H:Y.248 MGP.35: 14 residues within 4Å: Chain I: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285 Ligands: SAH.34, MG.36 16 PLIP interactions: 16 interactions with chain I Hydrogen bonds: I:R.41, I:R.70, I:R.92, I:Y.285 Water bridges: I:N.35, I:N.35, I:A.40, I:R.41, I:R.41, I:D.152 Salt bridges: I:H.37, I:R.41, I:R.41, I:R.70, I:E.250 pi-Stacking: I:Y.248 MGP.39: 14 residues within 4Å: Chain J: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285 Ligands: SAH.38, MG.40 16 PLIP interactions: 16 interactions with chain J Hydrogen bonds: J:R.41, J:R.70, J:R.92, J:Y.285 Water bridges: J:N.35, J:N.35, J:A.40, J:R.41, J:R.41, J:D.152 Salt bridges: J:H.37, J:R.41, J:R.41, J:R.70, J:E.250 pi-Stacking: J:Y.248 MGP.43: 14 residues within 4Å: Chain K: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285 Ligands: SAH.42, MG.44 16 PLIP interactions: 16 interactions with chain K Hydrogen bonds: K:R.41, K:R.70, K:R.92, K:Y.285 Water bridges: K:N.35, K:N.35, K:A.40, K:R.41, K:R.41, K:D.152 Salt bridges: K:H.37, K:R.41, K:R.41, K:R.70, K:E.250 pi-Stacking: K:Y.248 MGP.47: 14 residues within 4Å: Chain L: H.37, A.40, R.41, R.70, R.92, D.152, Y.154, F.241, V.243, Y.248, E.250, Y.285 Ligands: SAH.46, MG.48 16 PLIP interactions: 16 interactions with chain L Hydrogen bonds: L:R.41, L:R.70, L:R.92, L:Y.285 Water bridges: L:N.35, L:N.35, L:A.40, L:R.41, L:R.41, L:D.152 Salt bridges: L:H.37, L:R.41, L:R.41, L:R.70, L:E.250 pi-Stacking: L:Y.248

12 x MG: MAGNESIUM ION(Non-functional Binders)

MG.4: 1 residues within 4Å: Ligands: MGP.3 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Ligands: MGP.7 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: MGP.11 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Ligands: MGP.15 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Ligands: MGP.19 No protein-ligand interaction detected (PLIP) MG.24: 1 residues within 4Å: Ligands: MGP.23 No protein-ligand interaction detected (PLIP) MG.28: 1 residues within 4Å: Ligands: MGP.27 No protein-ligand interaction detected (PLIP) MG.32: 1 residues within 4Å: Ligands: MGP.31 No protein-ligand interaction detected (PLIP) MG.36: 1 residues within 4Å: Ligands: MGP.35 No protein-ligand interaction detected (PLIP) MG.40: 1 residues within 4Å: Ligands: MGP.39 No protein-ligand interaction detected (PLIP) MG.44: 1 residues within 4Å: Ligands: MGP.43 No protein-ligand interaction detected (PLIP) MG.48: 1 residues within 4Å: Ligands: MGP.47 No protein-ligand interaction detected (PLIP)

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

2022-07-27

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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