SMTL ID : 8jce.1

Cryo-EM Structure of Chikungunya Virus Nonstructural Protein 1 with m7GpppAmU

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.6: 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.10: 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.14: 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.18: 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.22: 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.26: 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.30: 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.34: 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.38: 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.42: 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.46: 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 SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 13 residues within 4Å: Chain A: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 Ligands: YG4.3 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:G.65, A:G.65, A:R.85, A:S.86, A:D.89, A:R.92, A:D.138, A:D.138 Water bridges: A:R.41, A:A.67, A:A.67, A:Q.151, A:D.152 Salt bridges: A:R.70, A:R.92 SAH.7: 13 residues within 4Å: Chain B: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 Ligands: YG4.8 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:G.65, B:G.65, B:R.85, B:S.86, B:D.89, B:R.92, B:D.138, B:D.138 Water bridges: B:R.41, B:A.67, B:Q.151 Salt bridges: B:R.70, B:R.92 SAH.11: 13 residues within 4Å: Chain C: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 Ligands: YG4.12 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:G.65, C:G.65, C:R.85, C:S.86, C:D.89, C:R.92, C:D.138, C:D.138 Water bridges: C:R.41, C:A.67, C:Q.151 Salt bridges: C:R.70, C:R.92 SAH.15: 13 residues within 4Å: Chain D: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 Ligands: YG4.16 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:G.65, D:G.65, D:R.85, D:S.86, D:D.89, D:R.92, D:D.138, D:D.138 Water bridges: D:R.41, D:A.67, D:A.67, D:Q.151, D:D.152 Salt bridges: D:R.70, D:R.92 SAH.19: 13 residues within 4Å: Chain E: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 Ligands: YG4.20 13 PLIP interactions: 13 interactions with chain E Hydrogen bonds: E:G.65, E:G.65, E:R.85, E:S.86, E:D.89, E:R.92, E:D.138, E:D.138 Water bridges: E:R.41, E:A.67, E:Q.151 Salt bridges: E:R.70, E:R.92 SAH.23: 13 residues within 4Å: Chain F: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 Ligands: YG4.24 13 PLIP interactions: 13 interactions with chain F Hydrogen bonds: F:G.65, F:G.65, F:R.85, F:S.86, F:D.89, F:R.92, F:D.138, F:D.138 Water bridges: F:R.41, F:A.67, F:Q.151 Salt bridges: F:R.70, F:R.92 SAH.27: 13 residues within 4Å: Chain G: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 Ligands: YG4.28 15 PLIP interactions: 15 interactions with chain G Hydrogen bonds: G:G.65, G:G.65, G:R.85, G:S.86, G:D.89, G:R.92, G:D.138, G:D.138 Water bridges: G:R.41, G:A.67, G:A.67, G:Q.151, G:D.152 Salt bridges: G:R.70, G:R.92 SAH.31: 13 residues within 4Å: Chain H: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 Ligands: YG4.32 13 PLIP interactions: 13 interactions with chain H Hydrogen bonds: H:G.65, H:G.65, H:R.85, H:S.86, H:D.89, H:R.92, H:D.138, H:D.138 Water bridges: H:R.41, H:A.67, H:Q.151 Salt bridges: H:R.70, H:R.92 SAH.35: 13 residues within 4Å: Chain I: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 Ligands: YG4.36 13 PLIP interactions: 13 interactions with chain I Hydrogen bonds: I:G.65, I:G.65, I:R.85, I:S.86, I:D.89, I:R.92, I:D.138, I:D.138 Water bridges: I:R.41, I:A.67, I:Q.151 Salt bridges: I:R.70, I:R.92 SAH.39: 13 residues within 4Å: Chain J: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 Ligands: YG4.40 15 PLIP interactions: 15 interactions with chain J Hydrogen bonds: J:G.65, J:G.65, J:R.85, J:S.86, J:D.89, J:R.92, J:D.138, J:D.138 Water bridges: J:R.41, J:A.67, J:A.67, J:Q.151, J:D.152 Salt bridges: J:R.70, J:R.92 SAH.43: 13 residues within 4Å: Chain K: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 Ligands: YG4.44 13 PLIP interactions: 13 interactions with chain K Hydrogen bonds: K:G.65, K:G.65, K:R.85, K:S.86, K:D.89, K:R.92, K:D.138, K:D.138 Water bridges: K:R.41, K:A.67, K:Q.151 Salt bridges: K:R.70, K:R.92 SAH.47: 13 residues within 4Å: Chain L: G.65, R.70, P.83, R.85, S.86, D.89, R.92, T.137, D.138, Q.151, D.152, V.156 Ligands: YG4.48 13 PLIP interactions: 13 interactions with chain L Hydrogen bonds: L:G.65, L:G.65, L:R.85, L:S.86, L:D.89, L:R.92, L:D.138, L:D.138 Water bridges: L:R.41, L:A.67, L:Q.151 Salt bridges: L:R.70, L:R.92

12 x YG4: [(2~{R},3~{R},4~{R},5~{R})-5-(6-azanyl-7,8-dihydropurin-9-yl)-2-[[[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-4-methoxy-oxolan-3-yl] [(2~{R},3~{S},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

YG4.3: 19 residues within 4Å: Chain A: T.33, N.35, A.40, R.41, R.70, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285 Chain B: E.54, D.277, V.279, R.289 Ligands: SAH.2, MG.5 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B Hydrogen bonds: A:N.35, A:N.35, A:R.41, A:N.95, A:D.152, A:Y.248, A:Y.248, A:Y.285, B:D.277, B:V.279 Salt bridges: A:R.41, A:R.70, A:K.99, A:E.250 pi-Stacking: A:Y.248, A:Y.248 Water bridges: B:R.275, B:R.275 pi-Cation interactions: B:R.289 YG4.8: 20 residues within 4Å: Chain B: T.33, N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285 Chain C: E.54, D.277, V.279, R.289 Ligands: SAH.7, MG.9 23 PLIP interactions: 17 interactions with chain B, 6 interactions with chain C Hydrogen bonds: B:N.35, B:N.35, B:R.41, B:N.95, B:D.152, B:Y.248, B:Y.248, B:Y.285, C:D.277, C:V.279, C:R.289 Water bridges: B:N.35, B:D.36, B:D.36, C:R.275, C:R.275 Salt bridges: B:R.41, B:R.70, B:K.99, B:E.250 pi-Stacking: B:Y.248, B:Y.248 pi-Cation interactions: C:R.289 YG4.12: 19 residues within 4Å: Chain C: T.33, N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, T.246, Y.248, E.250, Y.285 Chain D: E.54, D.277, V.279, R.289 Ligands: SAH.11, MG.13 21 PLIP interactions: 15 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:N.35, C:N.35, C:R.41, C:R.41, C:N.95, C:D.152, C:Y.248, C:Y.248, C:Y.285, D:D.277, D:V.279, D:R.289 Salt bridges: C:R.41, C:R.70, C:K.99, C:E.250 pi-Stacking: C:Y.248, C:Y.248 Water bridges: D:R.275, D:R.275 pi-Cation interactions: D:R.289 YG4.16: 19 residues within 4Å: Chain D: T.33, N.35, A.40, R.41, R.70, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285 Chain E: E.54, D.277, V.279, R.289 Ligands: SAH.15, MG.17 19 PLIP interactions: 14 interactions with chain D, 5 interactions with chain E Hydrogen bonds: D:N.35, D:N.35, D:R.41, D:N.95, D:D.152, D:Y.248, D:Y.248, D:Y.285, E:D.277, E:V.279 Salt bridges: D:R.41, D:R.70, D:K.99, D:E.250 pi-Stacking: D:Y.248, D:Y.248 Water bridges: E:R.275, E:R.275 pi-Cation interactions: E:R.289 YG4.20: 19 residues within 4Å: Chain E: T.33, N.35, A.40, R.41, R.70, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285 Chain F: E.54, D.277, V.279, R.289 Ligands: SAH.19, MG.21 23 PLIP interactions: 17 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:N.35, E:N.35, E:R.41, E:N.95, E:D.152, E:Y.248, E:Y.248, E:Y.285, F:D.277, F:V.279, F:R.289 Water bridges: E:N.35, E:D.36, E:D.36, F:R.275, F:R.275 Salt bridges: E:R.41, E:R.70, E:K.99, E:E.250 pi-Stacking: E:Y.248, E:Y.248 pi-Cation interactions: F:R.289 YG4.24: 19 residues within 4Å: Chain F: T.33, N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, T.246, Y.248, E.250, Y.285 Chain G: E.54, D.277, V.279, R.289 Ligands: SAH.23, MG.25 21 PLIP interactions: 15 interactions with chain F, 6 interactions with chain G Hydrogen bonds: F:N.35, F:N.35, F:R.41, F:R.41, F:N.95, F:D.152, F:Y.248, F:Y.248, F:Y.285, G:D.277, G:V.279, G:R.289 Salt bridges: F:R.41, F:R.70, F:K.99, F:E.250 pi-Stacking: F:Y.248, F:Y.248 Water bridges: G:R.275, G:R.275 pi-Cation interactions: G:R.289 YG4.28: 19 residues within 4Å: Chain G: N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285 Chain H: E.54, D.277, V.279, R.289 Ligands: SAH.27, MG.29 18 PLIP interactions: 4 interactions with chain H, 14 interactions with chain G Hydrogen bonds: H:D.277, H:V.279, G:N.35, G:N.35, G:R.41, G:N.95, G:D.152, G:Y.248, G:Y.248, G:Y.285 Water bridges: H:R.275 pi-Cation interactions: H:R.289 Salt bridges: G:R.41, G:R.70, G:K.99, G:E.250 pi-Stacking: G:Y.248, G:Y.248 YG4.32: 20 residues within 4Å: Chain H: T.33, N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285 Chain I: E.54, D.277, V.279, R.289 Ligands: SAH.31, MG.33 22 PLIP interactions: 17 interactions with chain H, 5 interactions with chain I Hydrogen bonds: H:N.35, H:N.35, H:R.41, H:N.95, H:D.152, H:Y.248, H:Y.248, H:Y.285, I:D.277, I:V.279 Water bridges: H:N.35, H:D.36, H:D.36, I:R.275, I:R.275 Salt bridges: H:R.41, H:R.70, H:K.99, H:E.250 pi-Stacking: H:Y.248, H:Y.248 pi-Cation interactions: I:R.289 YG4.36: 19 residues within 4Å: Chain I: T.33, N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, T.246, Y.248, E.250, Y.285 Chain J: E.54, D.277, V.279, R.289 Ligands: SAH.35, MG.37 21 PLIP interactions: 15 interactions with chain I, 6 interactions with chain J Hydrogen bonds: I:N.35, I:N.35, I:R.41, I:R.41, I:N.95, I:D.152, I:Y.248, I:Y.248, I:Y.285, J:D.277, J:V.279, J:R.289 Salt bridges: I:R.41, I:R.70, I:K.99, I:E.250 pi-Stacking: I:Y.248, I:Y.248 Water bridges: J:R.275, J:R.275 pi-Cation interactions: J:R.289 YG4.40: 18 residues within 4Å: Chain J: N.35, A.40, R.41, R.70, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285 Chain K: E.54, D.277, V.279, R.289 Ligands: SAH.39, MG.41 18 PLIP interactions: 14 interactions with chain J, 4 interactions with chain K Hydrogen bonds: J:N.35, J:N.35, J:R.41, J:N.95, J:D.152, J:Y.248, J:Y.248, J:Y.285, K:D.277, K:V.279 Salt bridges: J:R.41, J:R.70, J:K.99, J:E.250 pi-Stacking: J:Y.248, J:Y.248 Water bridges: K:R.275 pi-Cation interactions: K:R.289 YG4.44: 20 residues within 4Å: Chain K: T.33, N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, F.241, T.246, Y.248, E.250, Y.285 Chain L: E.54, D.277, V.279, R.289 Ligands: SAH.43, MG.45 22 PLIP interactions: 5 interactions with chain L, 17 interactions with chain K Hydrogen bonds: L:D.277, L:V.279, K:N.35, K:N.35, K:R.41, K:N.95, K:D.152, K:Y.248, K:Y.248, K:Y.285 Water bridges: L:R.275, L:R.275, K:N.35, K:D.36, K:D.36 pi-Cation interactions: L:R.289 Salt bridges: K:R.41, K:R.70, K:K.99, K:E.250 pi-Stacking: K:Y.248, K:Y.248 YG4.48: 19 residues within 4Å: Chain A: E.54, D.277, V.279, R.289 Chain L: T.33, N.35, A.40, R.41, R.70, N.95, K.99, D.152, Y.154, T.246, Y.248, E.250, Y.285 Ligands: MG.4, SAH.47 21 PLIP interactions: 15 interactions with chain L, 6 interactions with chain A Hydrogen bonds: L:N.35, L:N.35, L:R.41, L:R.41, L:N.95, L:D.152, L:Y.248, L:Y.248, L:Y.285, A:D.277, A:V.279, A:R.289 Salt bridges: L:R.41, L:R.70, L:K.99, L:E.250 pi-Stacking: L:Y.248, L:Y.248 Water bridges: A:R.275, A:R.275 pi-Cation interactions: A:R.289

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

MG.4: 1 residues within 4Å: Ligands: YG4.48 No protein-ligand interaction detected (PLIP) MG.5: 2 residues within 4Å: Chain B: D.277 Ligands: YG4.3 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain C: D.277 Ligands: YG4.8 No protein-ligand interaction detected (PLIP) MG.13: 1 residues within 4Å: Ligands: YG4.12 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain E: D.277 Ligands: YG4.16 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Chain F: D.277 Ligands: YG4.20 No protein-ligand interaction detected (PLIP) MG.25: 1 residues within 4Å: Ligands: YG4.24 No protein-ligand interaction detected (PLIP) MG.29: 2 residues within 4Å: Chain H: D.277 Ligands: YG4.28 No protein-ligand interaction detected (PLIP) MG.33: 2 residues within 4Å: Chain I: D.277 Ligands: YG4.32 No protein-ligand interaction detected (PLIP) MG.37: 1 residues within 4Å: Ligands: YG4.36 No protein-ligand interaction detected (PLIP) MG.41: 2 residues within 4Å: Chain K: D.277 Ligands: YG4.40 No protein-ligand interaction detected (PLIP) MG.45: 2 residues within 4Å: Chain L: D.277 Ligands: YG4.44 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Law, M.C.Y. et al., Chikungunya virus nonstructural protein 1 is a versatile RNA capping and decapping enzyme. J.Biol.Chem. (2023)

Release Date

2023-11-15

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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