SMTL ID : 1qvj.1

structure of NUDT9 complexed with ribose-5-phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

monomer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: E.32, W.33, Q.34, D.35 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.34, A:D.35, A:D.35 Water bridges: A:E.32 SO4.2: 5 residues within 4Å: Chain A: Q.56, I.57, S.58, R.88, W.107 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.56, A:I.57, A:S.58 Salt bridges: A:R.88 SO4.3: 3 residues within 4Å: Chain A: E.68, K.69, K.76 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.69 Salt bridges: A:K.76 SO4.4: 3 residues within 4Å: Chain A: K.145, W.152, K.250 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:K.145, A:K.250, A:K.252 SO4.5: 2 residues within 4Å: Chain A: K.271, W.281 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.281 Water bridges: A:K.271, A:K.271 Salt bridges: A:K.271

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain A: G.156, G.157 Ligands: MG.7, RP5.9 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.156, H2O.4, H2O.8 MG.7: 2 residues within 4Å: Chain A: E.172 Ligands: MG.6 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.172, H2O.4, H2O.4, H2O.7

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.8: 6 residues within 4Å: Chain A: W.120, K.128, K.136, H.137, R.277, D.278 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.120, A:H.137, A:H.137 Water bridges: A:R.277, A:R.277

1 x RP5: 5-O-phosphono-beta-D-ribofuranose(Non-covalent)

RP5.9: 12 residues within 4Å: Chain A: A.112, D.114, R.146, G.157, M.158, V.211, D.213, R.215, T.224, Y.263, H.266 Ligands: MG.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.114, A:D.213, A:D.213, A:T.224, A:Y.263 Water bridges: A:R.146, A:G.156, A:H.266 Salt bridges: A:R.146, A:R.215, A:R.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, B.W. et al., The crystal structure and mutational analysis of human NUDT9. J.Mol.Biol. (2003)

Release Date

2003-09-16

Peptides

ADP-ribose pyrophosphatase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

ADP-ribose pyrophosphatase

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