SMTL ID : 4qto.1

1.65 Angstrom resolution crystal structure of betaine aldehyde dehydrogenase (betB) from Staphylococcus aureus with BME-modified Cys289 and PEG molecule in active site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: K.484, G.487, I.488 Chain B: V.273 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.484 NA.8: 4 residues within 4Å: Chain A: V.273 Chain B: K.484, G.487, I.488 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.273 NA.13: 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.17: 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

5 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 6 residues within 4Å: Chain A: A.131, Y.182, F.307, V.312, H.472, Y.474 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.474 PGE.3: 4 residues within 4Å: Chain A: S.366, Y.367, V.370, R.409 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.409, A:R.409 PGE.9: 6 residues within 4Å: Chain A: W.517 Chain B: A.131, Y.182, F.307, H.472, Y.474 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.474, B:Y.474 PGE.14: 6 residues within 4Å: Chain C: A.131, Y.182, F.307, H.472, Y.474 Chain D: W.517 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Y.474 PGE.18: 6 residues within 4Å: Chain D: A.131, Y.182, F.307, C.313, H.472, Y.474 1 PLIP interactions: 1 interactions with chain D Water bridges: D:Y.182

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

PEG.4: 3 residues within 4Å: Chain A: S.32, W.41, E.221 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.32, A:E.221 PEG.5: 8 residues within 4Å: Chain A: P.179, W.180, G.257, G.258, C.313, H.360, K.363, F.416 2 PLIP interactions: 2 interactions with chain A Water bridges: A:W.180, A:K.363 PEG.6: 5 residues within 4Å: Chain A: S.85, G.86, E.87, Q.90, E.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.85, A:E.87 PEG.10: 4 residues within 4Å: Chain B: G.86, E.87, Q.90, E.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.91 PEG.11: 7 residues within 4Å: Chain B: P.179, G.257, G.258, C.313, H.360, K.363, F.416 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.360 Water bridges: B:W.180 PEG.19: 4 residues within 4Å: Chain D: S.85, G.86, E.87, E.91 1 PLIP interactions: 1 interactions with chain D Water bridges: D:S.85

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

TRS.7: 5 residues within 4Å: Chain A: E.127, A.348, T.350, E.351 Chain B: W.517 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.348, B:W.517 Water bridges: A:T.350, A:T.350 TRS.12: 6 residues within 4Å: Chain A: W.517 Chain B: E.127, A.348, D.349, T.350, E.351 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:W.517, B:A.348 Water bridges: B:A.348, B:T.350, B:E.351

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

PG4.15: 4 residues within 4Å: Chain C: S.366, Y.367, V.370, R.409 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.366, C:R.409, C:R.409

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

EDO.16: 6 residues within 4Å: Chain C: P.179, W.180, G.257, G.258, C.313, F.416 1 PLIP interactions: 1 interactions with chain C Water bridges: C:W.180

Links

RCSB   PDBe   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)

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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