SMTL ID : 8vuo.1

Crystal structure of SARS-CoV-2 nsp16/nsp10 in complex with Cap-1 RNA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.39 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: N.198 No protein-ligand interaction detected (PLIP) MG.14: 1 residues within 4Å: Chain C: N.198 No protein-ligand interaction detected (PLIP)

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

SAH.2: 19 residues within 4Å: Chain A: N.43, Y.47, G.71, G.73, S.74, P.80, G.81, D.99, L.100, N.101, G.113, D.114, C.115, D.130, M.131, Y.132, F.149 Chain E: A.1, U.2 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.71, A:G.73, A:S.74, A:G.81, A:L.100, A:N.101, A:D.114, A:C.115, A:Y.132 Water bridges: A:G.71, A:T.82, A:D.99, A:F.149 SAH.15: 21 residues within 4Å: Chain C: N.43, Y.47, G.71, A.72, G.73, S.74, P.80, G.81, D.99, L.100, N.101, G.113, D.114, C.115, D.130, M.131, Y.132, F.149 Chain F: A.1, U.2 Ligands: EDO.21 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:G.71, C:G.73, C:G.81, C:L.100, C:N.101, C:D.114, C:C.115, C:Y.132 Water bridges: C:N.43, C:G.71

16 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 5 residues within 4Å: Chain A: D.102, F.103, T.110, I.112 Chain B: H.80 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: R.255, G.256, T.257, A.258, R.279 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: L.14, Y.15, Q.18, F.230 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: T.136, K.137, N.138, V.139, T.140, H.174 Ligands: EDO.7, M7G.25 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: T.140, K.141, E.142, N.143, H.174 Ligands: EDO.6 Ligand excluded by PLIP EDO.10: 1 residues within 4Å: Chain B: C.90 Ligand excluded by PLIP EDO.11: 2 residues within 4Å: Chain B: V.21, P.84 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain B: I.38, T.39, N.40, C.41, N.105, P.107 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain B: I.55, F.89, C.90, D.91, K.95 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain C: T.56, L.57, T.58, W.189 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain C: R.255, G.256, T.257, A.258, R.279 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain C: K.123, Q.159, K.160 Ligand excluded by PLIP EDO.19: 9 residues within 4Å: Chain C: K.16, Q.18, R.19, Q.218, I.219, D.220, V.223, M.224, N.227 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain C: L.14, Y.15, Q.18, F.230 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain C: D.114, D.133, G.148, F.149 Ligands: SAH.15 Ligand excluded by PLIP EDO.24: 1 residues within 4Å: Chain D: C.90 Ligand excluded by PLIP

4 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain B: C.74, C.77, H.83, C.90 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.74, B:C.77, B:H.83, B:C.90 ZN.9: 4 residues within 4Å: Chain B: C.117, C.120, C.128, C.130 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.117, B:C.120, B:C.128, B:C.130 ZN.22: 4 residues within 4Å: Chain D: C.74, C.77, H.83, C.90 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.74, D:C.77, D:H.83, D:C.90 ZN.23: 4 residues within 4Å: Chain D: C.117, C.120, C.128, C.130 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.117, D:C.120, D:C.128, D:C.130

2 x M7G: 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE(Non-covalent)

M7G.25: 15 residues within 4Å: Chain A: K.24, C.25, D.26, L.27, Y.30, Y.132, K.137, T.172, E.173, H.174, S.175, S.201, S.202 Chain E: A.1 Ligands: EDO.6 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:K.24, A:L.27, A:Y.30, A:K.137, A:T.172, A:H.174, A:S.175, A:S.202 Water bridges: A:D.26 Salt bridges: A:K.137, A:K.137 pi-Stacking: A:Y.30, A:Y.30 pi-Cation interactions: A:K.24 M7G.26: 14 residues within 4Å: Chain C: K.24, C.25, D.26, L.27, Y.30, Y.132, K.137, T.172, E.173, H.174, S.175, S.201, S.202 Chain F: A.1 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:K.24, C:L.27, C:Y.30, C:Y.132, C:K.137, C:T.172, C:T.172, C:H.174, C:S.175, C:S.202 Water bridges: C:G.31 Salt bridges: C:K.137, C:K.137 pi-Stacking: C:Y.30, C:Y.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Misra, A. et al., Crystal structure of SARS-CoV-2 nsp16/nsp10 in complex with Cap-1 RNA. To Be Published

Release Date

2025-02-05

Peptides

2'-O-methyltransferase: AC
Non-structural protein 10: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

2'-O-methyltransferase

Non-structural protein 10

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