SMTL ID : 4mpy.1 (1 other biounit)

1.85 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) from Staphylococcus aureus (IDP00699) in complex with NAD+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 26 residues within 4Å: Chain A: I.177, T.178, P.179, W.180, N.181, K.204, P.205, S.206, E.207, G.237, G.241, D.242, F.255, G.257, G.258, T.261, H.264, I.265, E.279, L.280, G.281, C.313, H.360, K.363, E.414, F.416 26 PLIP interactions: 26 interactions with chain A Hydrophobic interactions: A:P.179, A:W.180 Hydrogen bonds: A:T.178, A:N.181, A:K.204, A:E.207, A:G.237, A:D.242, A:G.257, A:G.258, A:G.258, A:E.279, A:H.360, A:K.363, A:E.414 Water bridges: A:W.180, A:E.207, A:S.238, A:D.242, A:D.242, A:I.259, A:T.261, A:T.261, A:T.261, A:T.261 pi-Stacking: A:F.416 NAD.4: 25 residues within 4Å: Chain B: I.177, T.178, P.179, W.180, N.181, K.204, P.205, S.206, E.207, G.237, G.241, D.242, F.255, G.257, G.258, T.261, H.264, I.265, E.279, G.281, C.313, H.360, K.363, E.414, F.416 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:P.179 Hydrogen bonds: B:T.178, B:N.181, B:K.204, B:E.207, B:G.237, B:D.242, B:D.242, B:G.257, B:G.258, B:G.258, B:T.261, B:E.279, B:H.360, B:K.363, B:K.363 Water bridges: B:W.180, B:E.207, B:I.259, B:I.259, B:T.261, B:T.261, B:E.359, B:E.359 pi-Stacking: B:F.416 NAD.7: 26 residues within 4Å: Chain C: I.177, T.178, P.179, W.180, N.181, K.204, P.205, S.206, E.207, G.237, G.241, D.242, F.255, G.257, G.258, T.261, H.264, I.265, E.279, L.280, G.281, C.313, H.360, K.363, E.414, F.416 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:P.179, C:F.416 Hydrogen bonds: C:T.178, C:N.181, C:K.204, C:E.207, C:G.237, C:D.242, C:G.257, C:G.258, C:G.258, C:E.279, C:H.360, C:K.363, C:K.363, C:E.414 Water bridges: C:W.180, C:E.207, C:I.259, C:T.261, C:T.261, C:T.261, C:T.261 NAD.10: 27 residues within 4Å: Chain D: I.177, T.178, P.179, W.180, N.181, K.204, P.205, S.206, E.207, G.237, S.238, G.241, D.242, F.255, G.257, G.258, T.261, H.264, I.265, E.279, L.280, G.281, C.313, H.360, K.363, E.414, F.416 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:P.179, D:W.180 Hydrogen bonds: D:T.178, D:N.181, D:K.204, D:E.207, D:G.237, D:D.242, D:G.257, D:G.258, D:G.258, D:T.261, D:E.279, D:H.360, D:K.363, D:K.363, D:E.414 Water bridges: D:I.259, D:E.260, D:T.261 pi-Stacking: D:F.416

8 x NA: SODIUM ION(Non-functional Binders)

NA.2: 3 residues within 4Å: Chain A: K.484, G.487 Chain B: V.273 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.487 NA.3: 4 residues within 4Å: Chain A: I.52, I.53, D.121, I.208 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.53 Water bridges: A:I.53 NA.5: 3 residues within 4Å: Chain A: V.273 Chain B: K.484, G.487 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.273 NA.6: 5 residues within 4Å: Chain B: I.52, I.53, D.121, I.208, T.209 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.208 Water bridges: B:I.53 NA.8: 3 residues within 4Å: Chain C: K.484, G.487 Chain D: V.273 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.273 NA.9: 5 residues within 4Å: Chain C: I.52, I.53, D.121, I.208, T.209 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.121, C:I.208 Water bridges: C:I.53 NA.11: 4 residues within 4Å: Chain C: V.273 Chain D: K.484, G.487, I.488 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.487 NA.12: 5 residues within 4Å: Chain D: I.52, I.53, D.121, I.208, T.209 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.121, D:I.208 Water bridges: D:I.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, C. et al., Structure-based mutational studies of substrate inhibition of betaine aldehyde dehydrogenase BetB from Staphylococcus aureus. Appl.Environ.Microbiol. (2014)

Release Date

2013-10-09

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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