SMTL ID : 2esd.1

Crystal Structure of thioacylenzyme intermediate of an Nadp Dependent Aldehyde Dehydrogenase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.55 Å

Oligo State

homo-tetramer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 23 residues within 4Å: Chain A: I.150, S.151, F.153, K.177, P.179, T.180, G.208, R.209, G.210, G.214, D.215, V.218, F.228, G.230, S.231, I.234, R.237, I.238, K.329, S.330, Y.333, P.378, F.379 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:S.151, A:T.180, A:G.210, A:D.215, A:D.215, A:S.231, A:R.237, A:K.329 Water bridges: A:S.211, A:D.215, A:S.330, A:S.330 Salt bridges: A:K.177 pi-Stacking: A:Y.333 NAP.3: 17 residues within 4Å: Chain B: S.151, F.153, K.177, P.179, T.180, G.208, G.210, G.214, D.215, V.218, F.228, S.231, I.234, R.237, I.238, K.329, Y.403 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:T.180, B:G.208, B:G.210, B:D.215, B:D.215, B:S.231, B:S.231, B:K.329, B:K.329, B:Y.403 Water bridges: B:Q.181 Salt bridges: B:K.177 NAP.5: 20 residues within 4Å: Chain C: I.150, S.151, F.153, K.177, P.179, T.180, G.208, G.210, G.214, D.215, V.218, F.228, G.230, S.231, G.233, I.234, R.237, I.238, K.329, Y.403 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:S.151, C:T.180, C:T.180, C:G.208, C:G.210, C:D.215, C:S.231, C:S.231, C:G.233, C:R.237, C:K.329, C:K.329 Water bridges: C:Q.181, C:T.232 Salt bridges: C:K.177 NAP.7: 19 residues within 4Å: Chain D: S.151, F.153, K.177, P.179, T.180, G.208, R.209, G.210, S.211, G.214, D.215, V.218, F.228, S.231, I.234, R.237, I.238, K.329, Y.403 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:S.151, D:T.180, D:T.180, D:G.208, D:G.210, D:D.215, D:D.215, D:S.231, D:S.231, D:K.329 Water bridges: D:G.208, D:T.232, D:R.237, D:E.377 Salt bridges: D:K.177

4 x G3H: GLYCERALDEHYDE-3-PHOSPHATE(Covalent)

G3H.2: 9 residues within 4Å: Chain A: R.103, N.154, Y.155, R.283, C.284, T.285, Q.436, R.437, G.438 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.154, A:Y.155, A:C.284, A:T.285, A:T.285, A:R.437, A:R.437 Water bridges: A:R.103, A:R.103 Salt bridges: A:R.103, A:R.283, A:R.437 G3H.4: 8 residues within 4Å: Chain B: R.103, N.154, Y.155, R.283, C.284, T.285, Q.436, R.437 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:N.154, B:Y.155, B:Y.155, B:C.284, B:T.285, B:T.285, B:R.437, B:R.437 Water bridges: B:R.103, B:R.103 Salt bridges: B:R.103, B:R.283, B:R.437 G3H.6: 9 residues within 4Å: Chain C: R.103, N.154, Y.155, R.283, C.284, T.285, Q.436, R.437, G.438 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:N.154, C:C.284, C:T.285, C:R.437, C:R.437 Water bridges: C:R.103, C:R.103, C:R.103, C:R.437 Salt bridges: C:R.103, C:R.283, C:R.437 G3H.8: 9 residues within 4Å: Chain D: R.103, N.154, Y.155, R.283, C.284, T.285, Q.436, R.437, G.438 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:N.154, D:C.284, D:T.285, D:T.285, D:R.437, D:R.437 Salt bridges: D:R.103, D:R.283, D:R.437

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

D'Ambrosio, K. et al., The first crystal structure of a thioacylenzyme intermediate in the ALDH family: new coenzyme conformation and relevance to catalysis. Biochemistry (2006)

Release Date

2006-05-02

Peptides

NADP-dependent glyceraldehyde-3-phosphate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

NADP-dependent glyceraldehyde-3-phosphate dehydrogenase

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