SMTL ID : 6s4g.2 (1 other biounit)

Crystal structure of the omega transaminase from Chromobacterium violaceum in complex with PMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-dimer

Ligands

2 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PMP.1: 14 residues within 4Å: Chain A: S.125, G.126, S.127, Y.159, H.160, G.161, E.232, D.265, V.267, I.268, K.294 Chain B: F.326, T.327 Ligands: PEG.2 14 PLIP interactions: 5 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:T.327, B:T.327, B:T.327, A:G.126, A:S.127, A:K.294 Water bridges: B:N.124, B:Y.328, A:S.127, A:Y.159, A:E.232 Hydrophobic interactions: A:E.232, A:V.267 pi-Stacking: A:Y.159 PMP.3: 13 residues within 4Å: Chain A: F.326, T.327 Chain B: S.125, G.126, S.127, Y.159, H.160, G.161, E.232, D.265, V.267, I.268, K.294 15 PLIP interactions: 6 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:T.327, A:T.327, A:T.327, B:S.125, B:G.126, B:S.127, B:K.294 Water bridges: A:N.124, A:T.327, A:Y.328, B:Y.159, B:E.232 Hydrophobic interactions: B:E.232, B:V.267 pi-Stacking: B:Y.159

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

PEG.2: 9 residues within 4Å: Chain A: F.28, L.65, W.66, Y.159, Y.174, A.237, R.422 Chain B: F.94 Ligands: PMP.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.66, A:Y.174, A:Y.174, A:R.422

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

EDO.4: 6 residues within 4Å: Chain A: F.94 Chain B: F.28, Y.159, Y.174, A.237, R.422 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.174, B:R.422 EDO.5: 4 residues within 4Å: Chain B: N.157, G.171, M.172, K.173 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.157, B:K.173 EDO.6: 7 residues within 4Å: Chain B: N.157, M.172, Y.174, A.237, G.238, C.424, G.425 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.174, B:Y.174, B:G.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruggieri, F. et al., Insight into the dimer dissociation process of the Chromobacterium violaceum (S)-selective amine transaminase. Sci Rep (2019)

Release Date

2019-07-17

Peptides

Probable aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Probable aminotransferase

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