SMTL ID : 7r1u.1

Crystal structure of SARS-CoV-2 nsp10/nsp16 in complex with the WZ16 inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 4IK: (2S,5S)-2,6-diamino-5-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl}hexanoic acid(Non-covalent)

4IK.1: 19 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, D.115, C.116, D.131, M.132, Y.133, F.150 Ligands: GTA.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:D.131 Hydrogen bonds: A:N.44, A:Y.48, A:G.72, A:G.82, A:L.101, A:N.102, A:D.115, A:C.116, A:D.131, A:Y.133 Salt bridges: A:H.70

1 x GTA: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE(Non-covalent)

GTA.2: 18 residues within 4Å: Chain A: C.26, D.27, L.28, Y.31, K.47, Y.133, P.135, K.138, K.171, T.173, E.174, H.175, S.176, N.199, S.202, S.203, E.204 Ligands: 4IK.1 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:D.27, A:D.27, A:L.28, A:K.47, A:K.47, A:Y.133, A:K.171, A:E.174, A:H.175, A:S.176, A:N.199, A:S.202, A:S.203, A:S.203 Salt bridges: A:H.175 pi-Stacking: A:Y.31 pi-Cation interactions: A:Y.31

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

MES.3: 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.4: 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.5: 4 residues within 4Å: Chain B: C.109, 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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