SMTL ID : 6j2v.1 (2 other biounits)

GABA aminotransferase from Corynebacterium glutamicum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x PLZ: 4-[({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)AMINO]BUTANOIC ACID(Non-covalent)

PLZ.1: 17 residues within 4Å: Chain A: I.94, S.154, G.155, A.156, Y.182, H.183, G.184, R.185, E.251, E.256, D.284, I.286, Q.287, K.313 Chain B: M.123, G.341, T.342 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:I.94, A:Y.182, A:E.251, A:I.286 Hydrogen bonds: A:G.155, A:A.156, A:E.256, A:Q.287, A:K.313, A:K.313, A:K.313, B:G.341, B:T.342, B:T.342, B:T.342 Water bridges: A:S.154, A:S.154, B:Y.343 Salt bridges: A:R.185 PLZ.5: 17 residues within 4Å: Chain A: G.341, T.342 Chain B: I.94, S.154, G.155, A.156, Y.182, H.183, G.184, R.185, Y.199, E.251, E.256, D.284, I.286, Q.287, K.313 21 PLIP interactions: 5 interactions with chain A, 16 interactions with chain B Hydrogen bonds: A:G.341, A:T.342, A:T.342, A:T.342, B:S.154, B:G.155, B:A.156, B:E.256, B:Q.287, B:K.313, B:K.313, B:K.313 Water bridges: A:Y.343, B:S.154, B:S.154 Hydrophobic interactions: B:I.94, B:Y.182, B:E.251, B:I.286 Salt bridges: B:R.185 pi-Stacking: B:Y.182 PLZ.7: 17 residues within 4Å: Chain C: I.94, S.154, G.155, A.156, Y.182, H.183, G.184, R.185, E.251, E.256, D.284, I.286, Q.287, K.313 Chain D: M.123, G.341, T.342 20 PLIP interactions: 15 interactions with chain C, 5 interactions with chain D Hydrophobic interactions: C:I.94, C:Y.182, C:E.251, C:I.286 Hydrogen bonds: C:S.154, C:G.155, C:A.156, C:Y.182, C:Q.287, C:K.313, C:K.313, C:K.313, D:G.341, D:T.342, D:T.342, D:T.342 Water bridges: C:S.154, C:S.154, D:Y.343 Salt bridges: C:R.185 PLZ.11: 17 residues within 4Å: Chain C: M.123, G.341, T.342 Chain D: I.94, S.154, G.155, A.156, Y.182, H.183, G.184, R.185, E.251, E.256, D.284, I.286, Q.287, K.313 19 PLIP interactions: 15 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:I.94, D:Y.182, D:E.251, D:I.286 Hydrogen bonds: D:G.155, D:A.156, D:Y.182, D:Q.287, D:K.313, D:K.313, D:K.313, C:G.341, C:T.342, C:T.342 Water bridges: D:S.154, D:S.154, C:Y.343 Salt bridges: D:R.185 pi-Stacking: D:Y.182

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 10 residues within 4Å: Chain A: C.121, F.122, M.123, Y.130, L.151, F.152, G.340, G.341, G.344 Chain B: L.63 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.122, A:M.123, A:L.151, A:G.341, A:G.344 Water bridges: A:Y.343 GOL.3: 7 residues within 4Å: Chain A: A.168, A.333, P.334, G.335, A.338 Chain B: S.201, G.202 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:R.197, B:R.197, B:S.201 Hydrogen bonds: A:G.335 GOL.4: 7 residues within 4Å: Chain A: S.201, G.202 Chain B: A.168, A.333, P.334, G.335, A.338 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.201, B:G.335 Water bridges: A:R.61 GOL.6: 9 residues within 4Å: Chain A: L.63 Chain B: F.122, M.123, Y.130, L.151, F.152, G.340, G.341, G.344 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:F.122, B:M.123, B:Y.130, B:Y.130, B:L.151, B:G.340, B:G.344 GOL.8: 9 residues within 4Å: Chain C: C.121, F.122, M.123, Y.130, L.151, G.340, G.341, G.344 Chain D: L.63 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:F.122, C:M.123, C:Y.130, C:L.151, C:L.151, C:G.344 Water bridges: C:Y.343 GOL.9: 5 residues within 4Å: Chain C: P.334, G.335, A.338 Chain D: S.201, G.202 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.335 Water bridges: C:P.336, D:R.61 GOL.10: 7 residues within 4Å: Chain C: S.201, G.202 Chain D: A.168, A.333, P.334, G.335, A.338 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Water bridges: C:S.201, D:A.333 Hydrogen bonds: D:G.335 GOL.12: 9 residues within 4Å: Chain C: L.63 Chain D: C.121, F.122, M.123, Y.130, L.151, G.340, G.341, G.344 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:M.123, D:Y.130, D:L.151, D:G.341, D:G.344 Water bridges: D:F.122, D:Y.343

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hong, J. et al., Crystal structure of gamma-aminobutyrate aminotransferase in complex with a PLP-GABA adduct from Corynebacterium glutamicum. Biochem.Biophys.Res.Commun. (2019)

Release Date

2020-01-15

Peptides

PLP-dependent aminotransferases: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PLP-dependent aminotransferases

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