SMTL ID : 6z6i.1 (3 other biounits)

SARS-CoV-2 Macrodomain in complex with ADP-HPD

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

2 x A1R: 5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE(Non-covalent)

A1R.1: 23 residues within 4Å: Chain A: A.22, D.23, I.24, A.39, A.40, N.41, K.45, H.46, G.47, G.48, G.49, V.50, A.51, L.127, S.129, A.130, G.131, I.132, F.133, A.155, F.157, L.161 Ligands: A1R.6 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:D.23, A:D.23, A:I.24, A:N.41, A:G.47, A:V.50, A:S.129, A:S.129, A:G.131, A:I.132, A:F.133, A:F.157 Water bridges: A:H.46, A:A.51, A:N.100, A:L.127, A:A.130 pi-Stacking: A:F.157, A:F.157 A1R.6: 6 residues within 4Å: Chain A: D.23, G.49, G.131, I.132, F.157 Ligands: A1R.1 3 PLIP interactions: 3 interactions with chain A Water bridges: A:E.26, A:E.26, A:G.49

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

EDO.2: 4 residues within 4Å: Chain A: L.76, K.77, G.80, S.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.77, A:S.81, A:S.81 EDO.3: 4 residues within 4Å: Chain A: G.9, K.20, N.21, Y.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.21, A:Y.162 Water bridges: A:Y.162 EDO.5: 3 residues within 4Å: Chain A: E.115, D.146, T.147 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.115, A:T.147

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 10 residues within 4Å: Chain A: N.41, V.42, V.78, V.97, G.98, P.99, N.100, K.103, E.105, F.133 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.42, A:G.98, A:N.100, A:K.103

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

NA.7: 3 residues within 4Å: Chain A: K.159, N.160, D.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.159, A:N.160, A:D.163 NA.8: 2 residues within 4Å: Chain A: D.136, I.138 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.136

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rack, J.G.M. et al., Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential. Open Biology (2020)

Release Date

2020-12-02

Peptides

Replicase polyprotein 1ab: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Replicase polyprotein 1ab

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