SMTL ID : 3ghh.1

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 1.94 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: 8 residues within 4Å: Chain A: K.89, T.90, E.92, N.170, L.173, V.202, D.204, R.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.92, A:E.92 NAG-NAG.2: 6 residues within 4Å: Chain B: K.89, T.90, L.93, N.170, V.202, D.204 No protein-ligand interaction detected (PLIP)

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

SO4.3: 3 residues within 4Å: Chain A: Q.45, R.48, Q.49 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.45, A:Q.49 Water bridges: A:R.48 Salt bridges: A:R.48 SO4.4: 6 residues within 4Å: Chain A: R.36, T.78, V.79, P.80 Chain B: R.192, P.193 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.78 Salt bridges: A:R.36, B:R.192 SO4.5: 5 residues within 4Å: Chain A: S.39, R.40, R.42 Chain B: P.193, R.228 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.42, B:R.228 SO4.6: 5 residues within 4Å: Chain A: R.228 Chain B: G.38, S.39, R.40, R.42 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:S.39, B:R.40, B:R.40 Water bridges: B:G.38, A:R.228 Salt bridges: B:R.40, B:R.42, A:R.228 SO4.7: 3 residues within 4Å: Chain B: Q.45, R.48, Q.49 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.45, B:Q.49 Water bridges: B:R.48 Salt bridges: B:R.48

1 x 2NF: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy-hydroxyphosphoryl] [(2R,3S,4R,5R)-5-(3-carbamoylpyridin-1-ium-1yl)- 3-fluoro-,4- hydroxyoxolan-2-yl]methyl phosphate(Non-covalent)

2NF.8: 19 residues within 4Å: Chain B: F.86, W.87, S.88, K.89, K.91, L.106, E.107, D.116, W.137, R.138, S.147, W.150, E.151, S.154, S.181, I.182, F.183, R.185, Q.187 29 PLIP interactions: 29 interactions with chain B Hydrophobic interactions: B:W.150, B:W.150, B:W.150, B:I.182 Hydrogen bonds: B:W.87, B:S.88, B:K.89, B:E.107, B:D.116, B:D.116, B:W.137, B:R.138, B:E.151, B:S.154, B:I.182, B:F.183, B:R.185, B:R.185, B:Q.187 Water bridges: B:V.85, B:W.87, B:K.89, B:K.89, B:K.91, B:G.117 Salt bridges: B:K.89 pi-Stacking: B:W.137, B:W.137, B:W.137

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

2010-03-16

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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