SMTL ID : 5a7r.1

Human poly(ADP-ribose) glycohydrolase in complex with synthetic dimeric ADP-ribose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

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)

AR6.1: 22 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, N.311, Y.347, Y.350, N.424, G.426, C.427, G.428, A.429, F.430, F.457 Ligands: AR6.2, GOL.13 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:I.281, A:E.282, A:N.295, A:N.295, A:G.299, A:Q.309, A:N.311, A:Y.350, A:N.424, A:G.426, A:G.426, A:G.428, A:A.429, A:F.430 Water bridges: A:Q.309, A:E.310, A:Y.347, A:N.424, A:T.456, A:F.457 pi-Stacking: A:F.457 AR6.2: 14 residues within 4Å: Chain A: R.218, G.301, S.304, A.305, G.306, L.307, V.308, N.311, A.351, A.429 Ligands: AR6.1, SO4.6, GOL.14, GOL.18 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.295, A:A.305, A:G.306, A:L.307, A:V.308, A:N.311 Water bridges: A:S.304, A:S.304 Salt bridges: A:R.218, A:R.218

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

BME.3: 1 residues within 4Å: Chain A: C.158 No protein-ligand interaction detected (PLIP)

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

SO4.4: 5 residues within 4Å: Chain A: I.39, R.40, V.41, D.42, F.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.41, A:D.42 SO4.5: 1 residues within 4Å: Chain A: K.122 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.122 SO4.6: 2 residues within 4Å: Chain A: A.305 Ligands: AR6.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.305 SO4.7: 5 residues within 4Å: Chain A: E.14, E.15, M.16, R.17, R.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.14 Water bridges: A:R.18, A:R.18 Salt bridges: A:R.21 SO4.8: 4 residues within 4Å: Chain A: H.332, E.394, K.395, R.398 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.332, A:K.395 SO4.9: 3 residues within 4Å: Chain A: Y.119, R.199, N.201 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.90, A:R.199, A:N.201 Water bridges: A:R.90, A:N.116, A:N.116, A:N.201, A:A.202 Salt bridges: A:R.199 SO4.10: 2 residues within 4Å: Chain A: W.61, R.199 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.199

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 8 residues within 4Å: Chain A: E.282, Q.290, R.313, N.317, Q.343, D.362, S.364, T.374 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Q.290, A:Q.290, A:R.313, A:N.317, A:Q.343, A:S.364, A:T.374 Water bridges: A:R.313, A:N.317, A:S.364 GOL.12: 7 residues within 4Å: Chain A: E.264, R.265, C.266, E.267, T.479, D.482, K.485 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.482, A:D.482, A:K.485, A:K.485 GOL.13: 6 residues within 4Å: Chain A: N.424, C.427, G.428, D.459, L.462 Ligands: AR6.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.424, A:C.427, A:D.459, A:D.459 GOL.14: 4 residues within 4Å: Chain A: A.351, E.352, A.429 Ligands: AR6.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.429 GOL.15: 6 residues within 4Å: Chain A: H.383, F.384, R.385, R.386, D.389, K.395 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.385, A:R.386, A:D.389, A:K.395 GOL.16: 5 residues within 4Å: Chain A: R.240, A.244, P.246, E.342, R.372 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.342, A:R.372 Water bridges: A:A.244 GOL.17: 6 residues within 4Å: Chain A: N.63, K.67, L.169, E.207, Y.208, Y.211 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.63, A:K.67, A:E.207, A:E.207 Water bridges: A:E.207, A:S.210 GOL.18: 5 residues within 4Å: Chain A: N.295, H.383, R.385, F.430 Ligands: AR6.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.295, A:H.383, A:R.385 Water bridges: A:N.295, A:N.295, A:R.296 GOL.19: 7 residues within 4Å: Chain A: F.131, E.140, H.143, L.144, I.148, K.232, F.235 No protein-ligand interaction detected (PLIP) GOL.20: 5 residues within 4Å: Chain A: H.56, Y.57, P.160, N.161 Ligands: PPI.24 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.57 Water bridges: A:N.161, A:N.161 GOL.21: 3 residues within 4Å: Chain A: Q.106, K.109, I.129 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.106, A:Q.106, A:K.109

6 x PPI: PROPANOIC ACID(Non-covalent)

PPI.22: 6 residues within 4Å: Chain A: Y.76, R.90, K.114, Y.115, N.116, V.117 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.117 Hydrogen bonds: A:V.117 Water bridges: A:A.118 Salt bridges: A:R.90 PPI.23: 2 residues within 4Å: Chain A: L.26, R.371 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.26 Salt bridges: A:R.371 PPI.24: 4 residues within 4Å: Chain A: Y.57, C.70, E.72 Ligands: GOL.20 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.57, A:E.72 PPI.25: 5 residues within 4Å: Chain A: Y.277, G.279, F.457, G.458 Ligands: PPI.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.279 Water bridges: A:F.457 PPI.26: 2 residues within 4Å: Chain A: S.210, R.296 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.296 PPI.27: 6 residues within 4Å: Chain A: T.280, Y.347, T.348, G.349, F.457 Ligands: PPI.25 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.280 Hydrogen bonds: A:G.349

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lambrecht, M.J. et al., Synthesis of Dimeric Adp-Ribose and its Structure with Human Poly(Adp-Ribose) Glycohydrolase. J.Am.Chem.Soc. (2015)

Release Date

2015-07-22

Peptides

POLY(ADP-RIBOSE) GLYCOHYDROLASE: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

POLY(ADP-RIBOSE) GLYCOHYDROLASE