SMTL ID : 7ult.1 (1 other biounit)

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer Apo-Form.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 3 residues within 4Å: Chain A: R.88, Q.89, L.91 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.91 NA.2: 1 residues within 4Å: Chain A: N.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.299, A:N.299 NA.12: 2 residues within 4Å: Chain B: T.104, N.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.104 NA.13: 2 residues within 4Å: Chain B: T.113, N.116 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.113 Water bridges: B:V.118

7 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 6 residues within 4Å: Chain A: Y.134, T.174, E.175, H.176, S.204 Ligands: FMT.9 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.134, A:T.174, A:E.175, A:H.176, A:S.204 Water bridges: A:E.175, A:S.204 FMT.4: 5 residues within 4Å: Chain A: K.18, W.192, R.218, E.219, I.221 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.218, A:R.218 Water bridges: A:K.18 FMT.5: 6 residues within 4Å: Chain A: R.68, N.124, K.125, E.286, N.287, N.288 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.68, A:R.68, A:K.125, A:N.288 Water bridges: A:E.286, A:N.288 FMT.6: 5 residues within 4Å: Chain A: V.120, H.121, T.122, F.158, K.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.121, A:T.122 FMT.7: 4 residues within 4Å: Chain A: A.123, K.125, Q.161, K.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.162 FMT.8: 4 residues within 4Å: Chain A: K.184, H.188, P.217, Q.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.220 Water bridges: A:E.219, A:I.221 FMT.9: 3 residues within 4Å: Chain A: S.203, S.204 Ligands: FMT.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.204, A:S.204 Water bridges: A:S.203, A:S.204

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain B: C.76, C.79, H.85, C.92 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.76, B:C.79, B:H.85, B:C.92 ZN.11: 4 residues within 4Å: Chain B: C.119, C.122, C.130, C.132 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.119, B:C.122, B:C.130, B:C.132

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer Apo-Form. To Be Published

Release Date

2022-04-13

Peptides

2'-O-methyltransferase: A
Non-structural protein 10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2'-O-methyltransferase

Non-structural protein 10

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