SMTL ID : 7kg1.1

Structure of human PARG complexed with PARG-002

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

monomer

Ligands

4 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.1: 8 residues within 4Å: Chain A: P.31, V.37, I.39, R.40, V.41, D.42, F.53, Q.165 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.41 pi-Cation interactions: A:F.53 DMS.2: 8 residues within 4Å: Chain A: E.264, R.265, C.266, E.267, T.479, G.481, D.482, K.485 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.479 Salt bridges: A:D.482 DMS.3: 8 residues within 4Å: Chain A: E.283, Q.343, H.360, E.361, D.362, G.363, S.364, T.374 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:D.362 DMS.5: 7 residues within 4Å: Chain A: Y.57, D.59, C.70, S.71, E.72, W.91, P.160 No protein-ligand interaction detected (PLIP)

1 x WDD: 1,3-dimethyl-8-{[2-(morpholin-4-yl)ethyl]amino}-3,7-dihydro-1H-purine-2,6-dione(Non-covalent)

WDD.4: 9 residues within 4Å: Chain A: T.280, I.281, E.282, F.293, Q.309, Y.347, Y.350, F.457 Ligands: SO4.13 6 PLIP interactions: 6 interactions with chain A Water bridges: A:N.424, A:N.424, A:N.424 pi-Stacking: A:Y.350, A:Y.350, A:F.457

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 8 residues within 4Å: Chain A: T.11, P.269, L.270, T.271, R.272, L.273, H.470, T.474 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.270, A:L.270, A:H.470 Water bridges: A:T.11, A:L.270 GOL.7: 10 residues within 4Å: Chain A: F.293, A.294, N.295, A.381, W.425, G.426, C.427, G.428, F.430 Ligands: SO4.13 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.294, A:N.295, A:G.426

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.8: 6 residues within 4Å: Chain A: R.90, Y.119, P.198, R.199, N.201, A.202 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.119, A:R.199, A:R.199, A:N.201, A:N.201 Water bridges: A:R.199

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 7 residues within 4Å: Chain A: R.90, L.93, K.114, Y.115, N.116, V.117, A.118 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.117 Water bridges: A:R.90, A:A.118 Salt bridges: A:R.90 SO4.10: 5 residues within 4Å: Chain A: H.35, S.177, T.251, T.253, W.369 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.177, A:S.177, A:T.253 Salt bridges: A:H.35 SO4.11: 4 residues within 4Å: Chain A: T.280, Y.347, T.348, G.349 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.347, A:G.349 Water bridges: A:T.280, A:T.280, A:Y.347 SO4.12: 7 residues within 4Å: Chain A: P.27, L.28, L.29, V.41, L.44, D.368, W.369 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.29, A:W.369 SO4.13: 8 residues within 4Å: Chain A: F.293, Y.350, N.424, G.426, C.427, G.428 Ligands: WDD.4, GOL.7 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Y.350, A:Y.350, A:C.427, A:C.427 Water bridges: A:Q.309, A:N.424, A:N.424, A:A.429

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brosey, C.A. et al., Targeting SARS-CoV-2 Nsp3 macrodomain structure with insights from human poly(ADP-ribose) glycohydrolase (PARG) structures with inhibitors. Prog.Biophys.Mol.Biol. (2021)

Release Date

2021-03-10

Peptides

Poly(ADP-ribose) glycohydrolase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Poly(ADP-ribose) glycohydrolase

Related Entries With Identical Sequence