SMTL ID : 6fyq.1

The crystal structure of a new transaminase from the marine bacterium Virgibacillus

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 15 residues within 4Å: Chain A: G.150, G.151, S.152, N.155, Y.184, H.185, G.186, E.247, D.280, V.282, I.283, K.309 Chain B: F.343, T.344 Ligands: EDO.3 15 PLIP interactions: 11 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:Y.184, A:E.247, A:V.282, A:V.282 Hydrogen bonds: A:G.151, A:S.152, A:S.152, A:N.155, A:K.309, B:T.344, B:T.344, B:T.344 Water bridges: A:E.153, B:Y.345 Salt bridges: A:K.309 PLP.6: 15 residues within 4Å: Chain A: F.343, T.344 Chain B: G.150, G.151, S.152, N.155, Y.184, H.185, G.186, E.247, D.280, V.282, I.283, K.309 Ligands: EDO.8 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.184, B:E.247, B:V.282, B:V.282 Hydrogen bonds: B:G.151, B:S.152, B:S.152, B:N.155, B:K.309, A:T.344, A:T.344, A:T.344 Water bridges: B:E.153, A:Y.345 Salt bridges: B:K.309

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

EDO.2: 6 residues within 4Å: Chain A: G.70, D.71, G.98, V.100 Chain B: K.111, K.112 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.98, B:K.112 EDO.3: 7 residues within 4Å: Chain A: F.52, Y.184, F.200, R.438, Y.442 Chain B: F.119 Ligands: PLP.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.438 EDO.4: 6 residues within 4Å: Chain A: R.267, I.301, P.302, D.303, S.324, P.326 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.301, A:S.324, A:S.324 Water bridges: A:D.303 EDO.7: 6 residues within 4Å: Chain A: K.111, K.112 Chain B: G.70, D.71, G.98, V.100 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.112, B:G.98 EDO.8: 7 residues within 4Å: Chain A: F.119 Chain B: F.52, Y.184, F.200, R.438, Y.442 Ligands: PLP.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.438 EDO.9: 6 residues within 4Å: Chain B: R.267, I.301, P.302, D.303, S.324, P.326 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.301, B:S.324, B:S.324

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

CL.5: 2 residues within 4Å: Chain A: K.357, A.360 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: K.357, A.360 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guidi, B. et al., Strategic single point mutation yields a solvent- and salt-stable transaminase from Virgibacillus sp. in soluble form. Sci Rep (2018)

Release Date

2018-12-12

Peptides

amine transaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

amine transaminase