SMTL ID : 2wox.1

Betaine aldehyde dehydrogenase from Pseudomonas aeruginosa with NAD(P) H-catalytic thiol adduct.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Covalent)

NDP.1: 25 residues within 4Å: Chain A: I.148, G.149, W.151, N.152, K.175, S.177, E.178, G.206, S.207, G.208, G.212, Q.213, F.226, T.227, G.228, G.229, T.232, V.236, E.251, L.252, G.253, C.285, E.386, F.388 Ligands: 7PE.6 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:T.227, A:E.251 Hydrogen bonds: A:G.149, A:N.152, A:N.152, A:K.175, A:E.178, A:G.206, A:G.208, A:G.229, A:T.232, A:T.232, A:C.285, A:E.386 Water bridges: A:R.209, A:T.230 Salt bridges: A:K.175 NDP.9: 28 residues within 4Å: Chain B: I.148, G.149, A.150, W.151, N.152, K.175, S.177, E.178, G.206, S.207, G.208, G.212, Q.213, F.226, T.227, G.228, G.229, T.232, V.236, E.251, L.252, G.253, C.285, E.386, F.388, L.414 Ligands: GOL.8, GOL.11 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:T.227 Hydrogen bonds: B:G.149, B:K.175, B:S.177, B:E.178, B:G.208, B:G.229, B:T.232, B:E.386 Water bridges: B:R.209, B:T.230, B:G.254, B:E.386 Salt bridges: B:K.175 NDP.18: 28 residues within 4Å: Chain C: I.148, G.149, A.150, W.151, N.152, I.157, K.175, S.177, E.178, G.206, S.207, G.208, G.212, Q.213, F.226, T.227, G.228, G.229, T.232, V.236, E.251, L.252, G.253, C.285, E.386, F.388, L.414 Ligands: GOL.23 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:A.150, C:I.157, C:T.227 Hydrogen bonds: C:G.149, C:K.175, C:E.178, C:G.208, C:G.229, C:T.232, C:E.251, C:L.252, C:E.386 Water bridges: C:R.209, C:Q.213, C:T.230, C:T.232, C:E.386 Salt bridges: C:K.175 NDP.29: 27 residues within 4Å: Chain D: I.148, G.149, A.150, W.151, N.152, K.175, S.177, E.178, G.206, G.208, G.212, Q.213, F.226, T.227, G.228, G.229, T.232, V.236, E.251, L.252, G.253, C.285, E.386, F.388, L.414 Ligands: GOL.33, GOL.34 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:T.227 Hydrogen bonds: D:G.149, D:K.175, D:E.178, D:G.208, D:G.229, D:T.230, D:T.232, D:T.232, D:E.251, D:E.386 Water bridges: D:R.209, D:Q.213 Salt bridges: D:K.175

8 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: T.25, I.26, D.92, V.179 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.92, A:D.92, A:V.179 K.3: 3 residues within 4Å: Chain A: K.456, G.459 Chain B: L.245 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:K.456, B:L.245, H2O.16 K.10: 3 residues within 4Å: Chain A: L.245 Chain B: K.456, G.459 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Metal complexes: B:K.456, B:G.459, A:L.245 K.17: 4 residues within 4Å: Chain B: T.25, I.26, D.92, V.179 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:T.25, B:D.92, B:V.179 K.19: 4 residues within 4Å: Chain C: T.25, I.26, D.92, V.179 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:T.25, C:I.26, C:D.92, C:V.179 K.20: 3 residues within 4Å: Chain C: K.456, G.459 Chain D: L.245 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: C:K.456, D:L.245, H2O.39 K.30: 4 residues within 4Å: Chain D: T.25, I.26, D.92, V.179 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.92, D:V.179 K.31: 3 residues within 4Å: Chain C: L.245 Chain D: K.456, G.459 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Metal complexes: C:L.245, D:K.456

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 7 residues within 4Å: Chain A: W.160, E.251, T.286, S.446, V.452, E.463 Ligands: 7PE.6 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain B: G.208, R.209, K.235 Ligands: NDP.9 Ligand excluded by PLIP GOL.11: 9 residues within 4Å: Chain B: W.160, E.251, T.286, I.437, S.446, V.452, E.463 Ligands: NDP.9, 7PE.16 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain B: A.60, M.62, A.64, R.67 Chain D: P.128 Ligand excluded by PLIP GOL.13: 4 residues within 4Å: Chain B: F.3, Q.6, K.186 Ligands: GOL.14 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain B: E.4, E.5, Q.6, K.7, Y.14 Ligands: GOL.13 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain C: F.3, E.4, Q.6, K.186 Ligand excluded by PLIP GOL.22: 5 residues within 4Å: Chain C: Y.153, Q.156, W.160 Ligands: GOL.23, GOL.25 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain C: W.160, E.251, E.463 Ligands: NDP.18, GOL.22 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain C: R.313, L.314, D.319, N.321, T.322 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain C: T.107, E.445, S.446 Ligands: GOL.22, 7PE.27 Ligand excluded by PLIP GOL.26: 3 residues within 4Å: Chain C: S.335, G.338, Y.339 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain D: E.4, E.5, Q.6, K.7, Y.14 Ligands: GOL.35 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain D: Q.156, V.284 Ligands: NDP.29, GOL.34 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain D: E.251, T.286, S.446, V.452 Ligands: NDP.29, GOL.33 Ligand excluded by PLIP GOL.35: 5 residues within 4Å: Chain D: F.3, E.4, Q.6, K.186 Ligands: GOL.32 Ligand excluded by PLIP

5 x 7PE: 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL(Non-functional Binders)

7PE.5: 8 residues within 4Å: Chain A: A.121, R.139, L.466, A.470 Chain D: A.121, E.123, L.466, A.470 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.123, D:E.123 7PE.6: 6 residues within 4Å: Chain A: Y.153, Q.156, I.157, W.160 Ligands: NDP.1, GOL.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.156 7PE.15: 10 residues within 4Å: Chain B: G.11, S.51, E.54, G.55, V.58, M.62, I.70, G.195, P.197, D.198 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.51, B:D.198 7PE.16: 7 residues within 4Å: Chain B: T.107, Q.156, W.160, G.444, E.445, S.446 Ligands: GOL.11 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.156, B:S.446 7PE.27: 11 residues within 4Å: Chain C: M.275, F.279, V.284, T.286, N.287, W.443, G.444, E.445 Chain D: Y.485, A.486 Ligands: GOL.25 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:T.286 Water bridges: C:Y.153 Hydrophobic interactions: D:Y.485

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

BME.7: 4 residues within 4Å: Chain A: L.306, Q.310, L.351, C.352 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.310 BME.28: 4 residues within 4Å: Chain C: L.306, Q.310, L.351, C.352 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz-Sanchez, A.G. et al., Novel NADPH-cysteine covalent adduct found in the active site of an aldehyde dehydrogenase. Biochem. J. (2011)

Release Date

2010-08-25

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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