SMTL ID : 7q9z.1

Crystal structure of Chromobacterium violaceum aminotransferase in complex with PLP-pyruvate adduct

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x AN7: (3E)-4-{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}-2-oxobut-3-enoic acid(Non-covalent)

AN7.1: 15 residues within 4Å: Chain A: L.93, W.94, S.153, G.154, S.155, Y.187, H.188, G.189, E.260, A.265, D.293, V.295, I.296, R.450 Ligands: EDO.3 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.187, A:V.295, A:V.295 Hydrogen bonds: A:G.154, A:S.155 Salt bridges: A:R.450 AN7.6: 14 residues within 4Å: Chain B: L.93, W.94, S.153, G.154, S.155, Y.187, H.188, G.189, E.260, D.293, V.295, I.296, R.450 Ligands: EDO.8 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.187, B:V.295, B:V.295 Hydrogen bonds: B:G.154, B:S.155 Salt bridges: B:R.450

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

EDO.2: 2 residues within 4Å: Chain A: E.218, W.241 No protein-ligand interaction detected (PLIP) EDO.3: 10 residues within 4Å: Chain A: E.260, I.262, Q.263, G.264, D.293, E.294, V.295, I.296, C.297 Ligands: AN7.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.260, A:G.264, A:E.294, A:I.296, A:C.297 Water bridges: A:A.265 EDO.7: 1 residues within 4Å: Chain B: W.241 No protein-ligand interaction detected (PLIP) EDO.8: 10 residues within 4Å: Chain B: E.260, I.262, Q.263, G.264, D.293, E.294, V.295, I.296, C.297 Ligands: AN7.6 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.262, B:G.264, B:E.294, B:I.296, B:C.297 EDO.9: 4 residues within 4Å: Chain B: V.270, R.408, G.409, V.410 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.409

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 2 residues within 4Å: Chain A: K.224, F.431 Ligand excluded by PLIP

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

NA.5: 4 residues within 4Å: Chain A: G.75, V.76, Y.77, E.468 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.76, A:E.468 NA.10: 3 residues within 4Å: Chain B: A.138, T.141, P.142 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:T.141

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Isupov, M.N. et al., Aminotransferase from Chromobacterium violaceum in complex with PLP-pyruvate adduct. To Be Published

Release Date

2022-11-23

Peptides

Probable aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

Probable aminotransferase

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