SMTL ID : 6yz1.1

The crystal structure of SARS-CoV-2 nsp10-nsp16 methyltransferase complex with Sinefungin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 20 residues within 4Å: Chain A: N.44, Y.48, H.70, G.72, A.73, G.74, S.75, P.81, G.82, D.100, L.101, N.102, G.114, D.115, C.116, D.131, M.132, Y.133, D.134, F.150 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.44, A:A.73, A:G.74, A:G.82, A:L.101, A:N.102, A:N.102, A:D.115, A:C.116, A:Y.133 Water bridges: A:G.72, A:D.100, A:D.131, A:D.131, A:F.150, A:F.150

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 5 residues within 4Å: Chain A: N.14, T.57, L.58, T.59, W.190 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.14, A:T.59, A:W.190

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain B: C.66, C.69, H.75, C.82 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.66, B:C.69, B:H.75, B:C.82 ZN.4: 5 residues within 4Å: Chain B: C.109, V.111, C.112, C.120, C.122 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.109, B:C.112, B:C.120, B:C.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Krafcikova, P. et al., Structural analysis of the SARS-CoV-2 methyltransferase complex involved in RNA cap creation bound to sinefungin. Nat Commun (2020)

Release Date

2020-05-13

Peptides

nsp16: A
nsp10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

nsp16

nsp10

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