SMTL ID : 7r1t.1

Crystal structure of SARS-CoV-2 nsp10/nsp16 in complex with the SS148 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 6NR: (2~{S})-2-azanyl-4-[[(2~{S},3~{S},4~{R},5~{R})-5-(4-azanyl-5-cyano-pyrrolo[2,3-d]pyrimidin-7-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylsulfanyl]butanoic acid(Non-covalent)

6NR.1: 19 residues within 4Å: Chain A: N.44, Y.48, 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 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:Y.48, A:G.72, A:A.73, A:G.74, A:G.82, A:L.101, A:D.115, A:C.116, A:D.131, A:Y.133 Water bridges: A:G.72

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 8 residues within 4Å: Chain A: Y.133, T.137, T.173, E.174, H.175, S.176, S.203 Ligands: PO4.3 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.133, A:T.173, A:E.174, A:E.174, A:E.174, A:H.175, A:S.176, A:S.203 Salt bridges: A:H.175 PO4.3: 3 residues within 4Å: Chain A: S.202, S.203 Ligands: PO4.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.203, A:S.203, A:S.203

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

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

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 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.6: 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

Klima, M. et al., Crystal structure of SARS-CoV-2 nsp10-nsp16 in complex with small molecule inhibitors, SS148 and WZ16. Protein Sci. (2022)

Release Date

2022-06-29

Peptides

2'-O-methyltransferase nsp16: A
Non-structural protein 10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2'-O-methyltransferase nsp16

Non-structural protein 10

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