SMTL ID : 2qe0.1

Thioacylenzyme Intermediate of GAPN from S. Mutans, New Data Integration and Refinement.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-tetramer

Ligands

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

G3H.1: 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, A:G.438 Water bridges: A:R.103 Salt bridges: A:R.103, A:R.283, A:R.437 G3H.3: 10 residues within 4Å: Chain B: R.103, N.154, Y.155, R.283, C.284, T.285, Q.436, R.437, G.438, F.444 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:N.154, B:Y.155, B:C.284, B:T.285, B:R.437, B:G.438 Water bridges: B:R.103 Salt bridges: B:R.103, B:R.283, B:R.437 G3H.5: 9 residues within 4Å: Chain C: R.103, N.154, Y.155, R.283, C.284, T.285, Q.436, R.437, G.438 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:N.154, C:C.284, C:T.285, C:R.437, C:R.437, C:G.438 Water bridges: C:R.103, C:Y.155 Salt bridges: C:R.103, C:R.283, C:R.437 G3H.7: 9 residues within 4Å: Chain D: R.103, N.154, Y.155, R.283, C.284, T.285, Q.436, R.437, G.438 11 PLIP interactions: 11 interactions with chain D Hydrogen bonds: D:N.154, D:C.284, D:T.285, D:T.285, D:R.437, D:R.437, D:G.438 Water bridges: D:R.103 Salt bridges: D:R.103, D:R.283, D:R.437

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

NAP.2: 26 residues within 4Å: Chain A: I.150, S.151, P.152, F.153, K.177, P.178, P.179, T.180, G.208, R.209, G.210, G.214, D.215, V.218, F.228, T.229, G.230, S.231, I.234, R.237, L.251, G.252, C.284, Y.333, E.377, F.379 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:S.151, A:F.153, A:T.180, A:G.208, A:G.210, A:D.215, A:D.215, A:S.231, A:L.251 Water bridges: A:Q.181, A:S.211, A:S.211, A:R.237, A:E.377 Salt bridges: A:K.177 NAP.4: 27 residues within 4Å: Chain B: I.150, S.151, P.152, F.153, K.177, P.178, P.179, T.180, G.208, R.209, G.210, G.214, D.215, V.218, F.228, T.229, G.230, S.231, I.234, R.237, L.251, G.252, C.284, Y.333, E.377, P.378, F.379 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.379, B:F.379 Hydrogen bonds: B:S.151, B:F.153, B:T.180, B:G.210, B:D.215, B:D.215, B:S.231, B:L.251, B:E.377 Water bridges: B:Q.181, B:D.215, B:T.232, B:T.232 Salt bridges: B:K.177 NAP.6: 24 residues within 4Å: Chain C: I.150, S.151, P.152, F.153, K.177, P.178, 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, L.251, G.252, Y.333, E.377, F.379 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:F.379 Hydrogen bonds: C:S.151, C:F.153, C:T.180, C:T.180, C:G.210, C:D.215, C:S.231, C:R.237, C:Y.333, C:E.377, C:E.377 Water bridges: C:S.211, C:T.232, C:T.232 Salt bridges: C:K.177 NAP.8: 25 residues within 4Å: Chain D: I.150, S.151, P.152, F.153, K.177, P.178, P.179, T.180, G.208, R.209, G.210, G.214, D.215, V.218, F.228, T.229, G.230, S.231, I.234, R.237, G.252, Y.333, E.377, P.378, F.379 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:F.379 Hydrogen bonds: D:S.151, D:F.153, D:T.180, D:T.180, D:G.210, D:D.215, D:S.231, D:L.251, D:E.377, D:E.377 Water bridges: D:Q.181, D:G.208, D:S.211, D:T.232, D:T.232, D:R.237 Salt bridges: D:K.177 pi-Stacking: D:F.379

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

2007-12-25

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

Related Entries With Identical Sequence