SMTL ID : 3gc6.1 (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 1.51 Å

Oligo State

homo-dimer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 7 residues within 4Å: Chain A: K.89, T.90, N.170, L.173, V.202, D.204, R.240 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain B: K.89, T.90, E.92, L.93, N.170, V.202, D.204 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.92

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

SO4.2: 4 residues within 4Å: Chain A: T.30, T.34 Chain B: R.40, S.41 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.41, B:S.41 Water bridges: A:T.30 SO4.3: 2 residues within 4Å: Chain A: R.100, R.102 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.100 Salt bridges: A:R.100, A:R.102 SO4.4: 4 residues within 4Å: Chain A: S.88, K.89, S.181, I.182 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.182 Water bridges: A:S.88, A:F.183 Salt bridges: A:K.89 SO4.6: 4 residues within 4Å: Chain B: G.38, S.39, R.40, R.42 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.39, B:R.40 Salt bridges: B:R.40, B:R.42 SO4.7: 4 residues within 4Å: Chain A: Q.45 Chain B: Q.45, R.48, Q.49 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.45, B:Q.49, A:Q.45 Salt bridges: B:R.48

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

2010-03-02

Peptides

Ecto-NAD+ glycohydrolase (CD38 molecule): AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ecto-NAD+ glycohydrolase (CD38 molecule)

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