SMTL ID : 7bf4.1

Crystal structure of SARS-CoV-2 macrodomain in complex with GMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

1 x 5GP: GUANOSINE-5'-MONOPHOSPHATE(Non-covalent)

5GP.1: 7 residues within 4Å: Chain A: N.41, K.45, G.47, G.48, G.49, I.132, F.133 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:K.45, A:G.47, A:G.48 Water bridges: A:A.39, A:G.49, A:G.49, A:G.49, A:G.49, A:V.50, A:V.50, A:V.50, A:I.132

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

EDO.2: 5 residues within 4Å: Chain A: F.7, S.8, G.9, Y.10, Y.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.10 EDO.3: 4 residues within 4Å: Chain A: K.12, L.13, T.14, D.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.14, A:D.15 EDO.4: 5 residues within 4Å: Chain A: D.23, I.24, G.49, V.50, F.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.23, A:I.24 EDO.5: 6 residues within 4Å: Chain A: A.39, L.127, L.128, S.129, A.130, G.131 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.128, A:A.130 Water bridges: A:S.129, A:I.132 EDO.6: 5 residues within 4Å: Chain A: V.50, P.126, A.155, V.156, F.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.157 Water bridges: A:L.127 EDO.7: 6 residues within 4Å: Chain A: I.107, Q.108, L.110, K.111, H.139, V.143 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.110, A:K.111, A:H.139 EDO.8: 3 residues within 4Å: Chain A: N.41, N.100, F.133 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.41, A:N.100 Water bridges: A:E.105 EDO.9: 2 residues within 4Å: Chain A: T.72, N.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.73 EDO.10: 5 residues within 4Å: Chain A: G.47, G.48, G.52, A.53, K.56 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.47 Water bridges: A:G.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ni, X. et al., Structural Insights into Plasticity and Discovery of Remdesivir Metabolite GS-441524 Binding in SARS-CoV-2 Macrodomain. Acs Med.Chem.Lett. (2021)

Release Date

2021-01-13

Peptides

NSP3 macrodomain: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NSP3 macrodomain

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