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 No protein-ligand interaction detected (PLIP) 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 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.32, A:E.221 Water bridges: A:S.32 PEG.5: 8 residues within 4Å: Chain A: P.179, W.180, G.257, G.258, C.313, H.360, K.363, F.416 4 PLIP interactions: 4 interactions with chain A Water bridges: A:W.180, A:W.180, A:I.259, 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 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.360 Water bridges: B:W.180, B:N.181, B:K.363, B:E.414 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 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:A.348, B:W.517 Water bridges: A:E.127, A:A.348, 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 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.348, A:W.517 Water bridges: B:A.348, B:T.350, B:E.351, 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   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

2014-07-16

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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