SMTL ID : 3zqa.1

CRYSTALLOGRAPHIC STRUCTURE OF BETAINE ALDEHYDE DEHYDROGENASE MUTANT C286A FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH NADPH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-tetramer

Ligands

23 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 3 residues within 4Å: Chain A: Y.340, E.387 Ligands: NDP.10 Ligand excluded by PLIP GOL.2: 4 residues within 4Å: Chain A: M.276, W.444, G.445 Ligands: PG4.5 Ligand excluded by PLIP GOL.3: 5 residues within 4Å: Chain A: F.4, E.5, Q.7, K.187 Ligands: GOL.4 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: E.5, E.6, Q.7, K.8, Y.15 Ligands: GOL.3 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: R.269, Q.422, N.442 Chain B: E.482, L.483, G.484 Chain C: A.425 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: S.336, G.339, Y.340, E.386 Ligand excluded by PLIP GOL.9: 7 residues within 4Å: Chain A: W.161, E.252, T.287, V.453, E.464 Ligands: PG4.5, EDO.8 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain B: M.276, F.280, G.445 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain B: Y.154, Q.157, V.285 Ligands: GOL.17 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain B: F.4, E.5, Q.7, K.187 Ligand excluded by PLIP GOL.16: 5 residues within 4Å: Chain B: E.5, E.6, Q.7, K.8, Y.15 Ligand excluded by PLIP GOL.17: 8 residues within 4Å: Chain B: W.161, E.252, T.287, I.438, S.447, V.453, E.464 Ligands: GOL.14 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain B: S.208, G.209, R.210 Ligands: NDP.20 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: S.336, G.339, Y.340, S.343 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain C: F.4, E.5, Q.7, K.187 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain C: W.161, E.252, V.453, E.464 Ligands: TOE.28, EDO.29 Ligand excluded by PLIP GOL.25: 5 residues within 4Å: Chain C: R.314, L.315, G.316, D.320, T.323 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain C: S.336, G.339, Y.340, S.343, E.386 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain D: E.5, E.6, Q.7, K.8, Y.15 Ligands: GOL.35 Ligand excluded by PLIP GOL.33: 5 residues within 4Å: Chain D: Y.154, Q.157, W.161, V.285 Ligands: GOL.34 Ligand excluded by PLIP GOL.34: 8 residues within 4Å: Chain D: W.161, E.252, T.287, I.438, S.447, V.453, E.464 Ligands: GOL.33 Ligand excluded by PLIP GOL.35: 4 residues within 4Å: Chain D: F.4, Q.7, K.187 Ligands: GOL.32 Ligand excluded by PLIP GOL.36: 4 residues within 4Å: Chain D: G.209, R.210, K.236 Ligands: NDP.37 Ligand excluded by PLIP

1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 10 residues within 4Å: Chain A: T.108, Y.154, Q.157, W.161, V.285, E.446, S.447 Ligands: GOL.2, EDO.8, GOL.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.157, A:S.447 Water bridges: A:E.464

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.8: 6 residues within 4Å: Chain A: N.153, V.285, A.286, T.287 Ligands: PG4.5, GOL.9 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.153, A:A.286, A:T.287 EDO.29: 6 residues within 4Å: Chain C: N.153, V.285, A.286, T.287 Ligands: GOL.24, TOE.28 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:N.153, C:N.153, C:A.286, C:T.287 Water bridges: C:T.287

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

NDP.10: 24 residues within 4Å: Chain A: I.149, G.150, A.151, 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, L.253, G.254, A.286, E.387, F.389 Ligands: GOL.1 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:A.151, A:W.152 Hydrogen bonds: A:G.150, A:K.176, A:E.179, A:G.209, A:Q.214, A:G.230, A:T.233, A:T.233, A:L.253 Water bridges: A:W.152, A:S.178, A:R.210, A:R.210, A:H.333, A:S.336 Salt bridges: A:K.176 pi-Stacking: A:F.389 NDP.20: 25 residues within 4Å: Chain B: I.149, G.150, A.151, 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, L.253, G.254, A.286, E.387, F.389 Ligands: GOL.18 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.151 Hydrogen bonds: B:G.150, B:K.176, B:S.178, B:E.179, B:E.179, B:G.209, B:G.230, B:T.233, B:L.253 Water bridges: B:H.333, B:S.336 Salt bridges: B:K.176 pi-Stacking: B:F.389 NDP.27: 24 residues within 4Å: Chain C: I.149, G.150, A.151, 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, L.253, G.254, A.286, E.387, F.389 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:A.151, C:W.152 Hydrogen bonds: C:G.150, C:K.176, C:S.178, C:E.179, C:S.208, C:G.209, C:G.230, C:T.233, C:L.253, C:E.387, C:E.387 Water bridges: C:W.152, C:R.210, C:R.210, C:T.233, C:H.333, C:S.336 Salt bridges: C:K.176 pi-Stacking: C:F.389 NDP.37: 23 residues within 4Å: Chain D: I.149, G.150, A.151, 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, L.253, A.286, E.387, F.389 Ligands: GOL.36 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:A.151, D:W.152 Hydrogen bonds: D:G.150, D:K.176, D:S.178, D:E.179, D:E.179, D:G.209, D:G.230, D:T.233, D:T.233, D:L.253, D:E.387 Water bridges: D:W.152, D:S.178, D:T.233, D:S.336 Salt bridges: D:K.176 pi-Stacking: D:F.389

8 x K: POTASSIUM ION(Non-covalent)

K.11: 4 residues within 4Å: Chain A: T.26, I.27, D.93, V.180 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:I.27, A:D.93, A:V.180, H2O.4 K.12: 3 residues within 4Å: Chain A: K.457, G.460 Chain B: L.246 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:K.457, A:G.460, B:L.246, H2O.14 K.21: 3 residues within 4Å: Chain A: L.246 Chain B: K.457, G.460 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:G.460, A:L.246, H2O.16, H2O.16 K.22: 4 residues within 4Å: Chain B: T.26, I.27, D.93, V.180 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:T.26, B:I.27, B:D.93, B:V.180, H2O.28 K.30: 4 residues within 4Å: Chain C: T.26, I.27, D.93, V.180 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:I.27, C:D.93, C:V.180, H2O.53 K.31: 3 residues within 4Å: Chain C: K.457, G.460 Chain D: L.246 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:L.246 K.38: 4 residues within 4Å: Chain D: T.26, I.27, D.93, V.180 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:I.27, D:D.93, D:V.180, H2O.60 K.39: 3 residues within 4Å: Chain C: L.246 Chain D: K.457, G.460 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.51

1 x TOE: 2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL(Non-covalent)

TOE.28: 8 residues within 4Å: Chain C: T.108, Q.157, I.158, W.161, E.446, S.447 Ligands: GOL.24, EDO.29 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.157, C:Q.157, C:S.447

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

2011-10-26

Peptides

BETAINE ALDEHYDE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

BETAINE ALDEHYDE DEHYDROGENASE