SMTL ID : 3p5s.1 (1 other biounit)

Structural insights into the catalytic mechanism of CD38: Evidence for a conformationally flexible covalent enzyme-substrate complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.1: 6 residues within 4Å: Chain A: K.120, T.121, N.201, L.204, V.233, D.235 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.201, A:D.235

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

SO4.2: 1 residues within 4Å: Chain A: R.259 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.259

1 x AVU: [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate(Non-covalent)

AVU.3: 15 residues within 4Å: Chain A: F.117, W.118, S.119, K.120, K.122, L.137, E.138, D.147, G.148, W.181, S.185, S.212, I.213, F.214, E.218 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:W.118, A:K.120, A:K.122, A:E.138, A:D.147, A:D.147, A:G.148, A:S.185, A:S.212, A:I.213, A:F.214 Water bridges: A:V.116, A:W.118, A:K.120, A:K.120, A:L.149 Salt bridges: A:K.120, A:K.120 pi-Stacking: A:W.181, A:W.181, A:W.181, A:W.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Egea, P.F. et al., Insights into the mechanism of bovine CD38/NAD+glycohydrolase from the X-ray structures of its Michaelis complex and covalently-trapped intermediates. Plos One (2012)

Release Date

2011-10-19

Peptides

CD38 molecule: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

CD38 molecule

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