SMTL ID : 4b1h.1

Structure of human PARG catalytic domain in complex with ADP-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.1: 2 residues within 4Å: Chain A: C.158, N.161 No protein-ligand interaction detected (PLIP)

1 x DTV: (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTV.2: 4 residues within 4Å: Chain A: P.261, C.266, K.268, Y.404 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.404, A:Y.404 Water bridges: A:E.262

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: N.295, R.296, H.383, F.430 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.295, A:R.296, A:H.383 GOL.4: 7 residues within 4Å: Chain A: F.131, E.140, H.143, L.144, I.148, K.232, F.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.140, A:L.144

2 x AR6: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE(Non-covalent)

AR6.5: 19 residues within 4Å: Chain A: T.280, I.281, E.282, F.293, A.294, N.295, G.300, V.308, Q.309, E.310, E.311, Y.350, N.424, G.426, C.427, G.428, A.429, F.430, F.457 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:I.281, A:E.282, A:N.295, A:N.295, A:Q.309, A:E.311, A:E.311, A:Y.347, A:Y.350, A:N.424, A:G.426, A:G.428, A:A.429, A:F.430 Water bridges: A:Q.309, A:E.310, A:N.424, A:T.456, A:F.457 pi-Stacking: A:F.457 AR6.6: 7 residues within 4Å: Chain A: P.31, V.37, I.39, R.40, V.41, D.42, F.53 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.39, A:V.41 Water bridges: A:Q.165 pi-Stacking: A:F.53, A:F.53

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

SO4.7: 5 residues within 4Å: Chain A: R.90, Y.119, P.198, R.199, N.201 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.119, A:R.199, A:N.201 Water bridges: A:R.90, A:R.90, A:Y.119, A:R.199 Salt bridges: A:R.90, A:R.199 SO4.8: 3 residues within 4Å: Chain A: W.61, K.67, R.199 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.61 Salt bridges: A:R.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tucker, J.A. et al., Structures of the Human Poly (Adp-Ribose) Glycohydrolase Catalytic Domain Confirm Catalytic Mechanism and Explain Inhibition by Adp-Hpd Derivatives. Plos One (2012)

Release Date

2012-12-19

Peptides

POLY(ADP-RIBOSE) GLYCOHYDROLASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

POLY(ADP-RIBOSE) GLYCOHYDROLASE

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