SMTL ID : 2wme.2 (1 other biounit)

Crystallographic structure of betaine aldehyde dehydrogenase from Pseudomonas aeruginosa

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 19 residues within 4Å: Chain A: I.149, G.150, W.152, K.176, S.178, E.179, G.207, S.208, G.209, G.213, Q.214, F.227, T.228, G.229, G.230, T.233, V.237 Ligands: BME.2, GOL.10 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.150, A:K.176, A:E.179, A:G.209, A:G.230, A:T.233 Water bridges: A:Q.214, A:T.233 Salt bridges: A:K.176 NAP.11: 18 residues within 4Å: Chain B: I.149, G.150, W.152, K.176, S.178, E.179, G.207, S.208, G.209, R.210, G.213, Q.214, F.227, T.228, G.229, G.230, T.233, V.237 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:G.150, B:E.179, B:G.209, B:R.210, B:G.230, B:T.233 Water bridges: B:R.210, B:T.233, B:T.233 Salt bridges: B:K.176 NAP.18: 18 residues within 4Å: Chain C: I.149, G.150, W.152, K.176, S.178, E.179, G.207, S.208, G.209, R.210, G.213, Q.214, F.227, T.228, G.229, G.230, T.233, V.237 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.150, C:K.176, C:E.179, C:G.209, C:G.230, C:T.233 Water bridges: C:R.210, C:R.210, C:Q.214, C:Q.214, C:T.233 Salt bridges: C:K.176 NAP.24: 18 residues within 4Å: Chain D: I.149, G.150, K.176, S.178, E.179, G.207, S.208, G.209, G.213, Q.214, T.217, F.227, T.228, G.229, G.230, T.233, V.237 Ligands: BME.25 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:G.150, D:K.176, D:P.177, D:E.179, D:G.209, D:Q.214, D:G.230 Water bridges: D:W.152, D:R.210 Salt bridges: D:K.176

3 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 7 residues within 4Å: Chain A: G.229, G.230, L.253, G.254, C.286, E.387 Ligands: NAP.1 No protein-ligand interaction detected (PLIP) BME.12: 6 residues within 4Å: Chain B: G.229, L.253, G.254, C.286, E.387, F.389 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.387 BME.25: 6 residues within 4Å: Chain D: G.229, G.230, G.254, C.286, E.387 Ligands: NAP.24 No protein-ligand interaction detected (PLIP)

8 x K: POTASSIUM ION(Non-covalent)

K.3: 4 residues within 4Å: Chain A: T.26, I.27, D.93, V.180 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.26, A:I.27, A:D.93, A:D.93, A:V.180 K.4: 4 residues within 4Å: Chain A: K.457, G.460, V.461 Chain B: L.246 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:K.457, A:G.460, B:L.246, H2O.15, H2O.24 K.13: 4 residues within 4Å: Chain B: T.26, I.27, D.93, V.180 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.26, B:I.27, B:D.93, B:D.93, B:V.180 K.14: 3 residues within 4Å: Chain A: L.246 Chain B: K.457, G.460 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:K.457, B:G.460, A:L.246, H2O.8, H2O.31 K.19: 4 residues within 4Å: Chain C: T.26, I.27, D.93, V.180 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:T.26, C:I.27, C:D.93, C:D.93, C:V.180 K.20: 3 residues within 4Å: Chain C: K.457, G.460 Chain D: L.246 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:K.457, C:G.460, D:L.246, H2O.53, H2O.54 K.26: 4 residues within 4Å: Chain D: T.26, I.27, D.93, V.180 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:T.26, D:I.27, D:D.93, D:D.93, D:V.180 K.27: 5 residues within 4Å: Chain C: L.246, E.248 Chain D: K.457, G.460, V.461 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:K.457, D:G.460, C:L.246, H2O.39

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: R.3, F.4, E.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.5, A:E.5 GOL.6: 4 residues within 4Å: Chain A: R.296, D.376, R.378, V.397 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.296, A:R.296, A:D.376 Water bridges: A:R.378, A:V.397, A:V.397 GOL.7: 6 residues within 4Å: Chain A: A.61, M.63, R.68 Chain C: P.129, L.130, R.131 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:M.63, A:R.68, A:R.68 Water bridges: A:A.62, C:E.132 GOL.8: 5 residues within 4Å: Chain A: E.5, E.6, Q.7, K.8, Y.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.8 Water bridges: A:Q.7, A:E.190 GOL.9: 4 residues within 4Å: Chain A: N.153, Q.157, V.285, C.286 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.153, A:Q.157, A:C.286 Water bridges: A:Y.154, A:G.445 GOL.10: 3 residues within 4Å: Chain A: G.209, R.210 Ligands: NAP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.209, A:R.210, A:R.210, A:R.210 GOL.15: 4 residues within 4Å: Chain B: W.161, E.252, L.415 Ligands: GOL.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.252, B:E.252 Water bridges: B:S.447 GOL.16: 6 residues within 4Å: Chain B: N.153, Y.154, Q.157, V.285, C.286 Ligands: GOL.15 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.153, B:Q.157, B:C.286 Water bridges: B:T.108, B:T.108 GOL.17: 5 residues within 4Å: Chain B: E.5, E.6, Q.7, K.8, Y.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.5, B:K.8 Water bridges: B:Q.7 GOL.21: 3 residues within 4Å: Chain C: T.23, E.25, K.37 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.23 GOL.22: 3 residues within 4Å: Chain C: F.4, Q.7, K.187 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.7, C:Q.7 Water bridges: C:K.187 GOL.23: 3 residues within 4Å: Chain C: Y.154, Q.157, V.285 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.157 Water bridges: C:N.153, C:G.445, C:S.447 GOL.28: 4 residues within 4Å: Chain D: E.6, Q.7, K.8, Y.15 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.8 Water bridges: D:Q.7, D:Q.7, D:Y.15, D:K.187 GOL.29: 2 residues within 4Å: Chain D: Y.154, Q.157 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Q.157 Water bridges: D:N.153

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gonzalez-Segura, L. et al., The Crystal Structure of a Ternary Complex of Betaine Aldehyde Dehydrogenase from Pseudomonas Aeruginosa Provides New Insight Into the Reaction Mechanism and Shows a Novel Binding Mode of the 2'- Phosphate of Nadp(+) and a Novel Cation Binding Site. J.Mol.Biol. (2009)

Release Date

2009-08-04

Peptides

BETAINE ALDEHYDE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

BETAINE ALDEHYDE DEHYDROGENASE

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