SMTL ID : 4qje.1

1.85 Angstrom resolution crystal structure of apo betaine aldehyde dehydrogenase (betB) G234S mutant from Staphylococcus aureus (IDP00699) with BME-free sulfinic acid form of Cys289

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 5 residues within 4Å: Chain A: I.49, I.50, D.118, I.205, T.206 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.50, A:D.118, A:D.118 NA.2: 3 residues within 4Å: Chain A: K.481, G.484 Chain B: V.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.481 NA.6: 5 residues within 4Å: Chain B: I.49, I.50, D.118, I.205, T.206 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.50, B:I.50 NA.7: 3 residues within 4Å: Chain A: V.270 Chain B: K.481, G.484 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.270 NA.9: 4 residues within 4Å: Chain C: I.49, I.50, D.118, I.205 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.50, C:D.118, C:D.118 NA.10: 3 residues within 4Å: Chain C: K.481, G.484 Chain D: V.270 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.484 NA.17: 5 residues within 4Å: Chain D: I.49, I.50, D.118, I.205, T.206 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.118 Water bridges: D:I.50 NA.18: 3 residues within 4Å: Chain C: V.270 Chain D: K.481, G.484 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.270

8 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 5 residues within 4Å: Chain A: S.82, G.83, E.84, Q.87, E.88 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.88 Water bridges: A:E.88 PEG.4: 5 residues within 4Å: Chain A: S.363, Y.364, V.367, R.406, E.410 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.406, A:R.406 Water bridges: A:S.363 PEG.8: 4 residues within 4Å: Chain B: G.83, E.84, Q.87, E.88 No protein-ligand interaction detected (PLIP) PEG.11: 3 residues within 4Å: Chain B: R.453 Chain C: T.507, N.508 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:R.453, C:T.507 PEG.12: 4 residues within 4Å: Chain C: S.363, Y.364, V.367, R.406 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.363, C:S.363, C:R.406, C:R.406 PEG.13: 4 residues within 4Å: Chain C: G.83, E.84, Q.87, E.88 No protein-ligand interaction detected (PLIP) PEG.19: 4 residues within 4Å: Chain D: G.83, E.84, Q.87, E.88 1 PLIP interactions: 1 interactions with chain D Water bridges: D:E.88 PEG.20: 1 residues within 4Å: Chain D: D.386 1 PLIP interactions: 1 interactions with chain D Water bridges: D:R.384

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 5 residues within 4Å: Chain A: E.124, A.345, D.346, T.347 Chain B: W.514 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.345, B:W.514 Water bridges: A:A.345, A:T.347, A:E.348, A:E.348, A:E.348 TRS.14: 4 residues within 4Å: Chain C: W.514 Chain D: E.124, A.345, T.347 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:D.346, C:W.514 Water bridges: D:A.345, D:T.347, D:E.348, D:E.348 TRS.15: 4 residues within 4Å: Chain C: E.124, A.345, T.347 Chain D: W.514 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:A.345, D:W.514 Water bridges: C:E.124, C:A.345, C:T.347

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.16: 5 residues within 4Å: Chain C: W.38, R.212, E.215, E.218, E.219 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:R.212, C:E.215, C:E.215, C:E.218 Water bridges: C:E.37, C:E.37, C:R.212, C:E.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Halavaty, A.S. et al., Structural and functional analysis of betaine aldehyde dehydrogenase from Staphylococcus aureus. Acta Crystallogr.,Sect.D (2015)

Release Date

2014-06-18

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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