SMTL ID : 6q8e.1

Crystal structure of branched-chain amino acid aminotransferase from Thermobaculum terrenum in PMP-form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-hexamer

Ligands

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

PMP.1: 18 residues within 4Å: Chain A: H.60, R.63, R.149, K.160, Y.165, E.194, T.196, G.197, S.198, C.199, L.218, S.220, I.221, T.222, C.257, G.258, T.259 Ligands: CL.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.218 Hydrogen bonds: A:K.160, A:K.160, A:Y.165, A:Y.165, A:S.220, A:I.221, A:T.222, A:T.222, A:T.259 Water bridges: A:R.63, A:R.63, A:Y.100 Salt bridges: A:H.60, A:R.63 PMP.7: 18 residues within 4Å: Chain B: H.60, R.63, R.149, K.160, Y.165, E.194, T.196, G.197, S.198, C.199, L.218, S.220, I.221, T.222, C.257, G.258, T.259 Ligands: CL.8 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.218 Hydrogen bonds: B:K.160, B:K.160, B:Y.165, B:Y.165, B:S.220, B:I.221, B:T.222, B:T.222, B:T.259 Water bridges: B:R.63, B:R.63, B:Y.100 Salt bridges: B:H.60, B:R.63 PMP.13: 18 residues within 4Å: Chain C: H.60, R.63, R.149, K.160, Y.165, E.194, T.196, G.197, S.198, C.199, L.218, S.220, I.221, T.222, C.257, G.258, T.259 Ligands: CL.14 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:L.218 Hydrogen bonds: C:K.160, C:K.160, C:Y.165, C:Y.165, C:S.220, C:I.221, C:T.222, C:T.222, C:T.259 Water bridges: C:R.63, C:R.63, C:Y.100 Salt bridges: C:H.60, C:R.63 PMP.19: 18 residues within 4Å: Chain D: H.60, R.63, R.149, K.160, Y.165, E.194, T.196, G.197, S.198, C.199, L.218, S.220, I.221, T.222, C.257, G.258, T.259 Ligands: CL.20 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:L.218 Hydrogen bonds: D:K.160, D:K.160, D:Y.165, D:S.220, D:I.221, D:T.222, D:T.259, D:T.259 Water bridges: D:R.63, D:R.63 Salt bridges: D:H.60, D:R.63 PMP.25: 18 residues within 4Å: Chain E: H.60, R.63, R.149, K.160, Y.165, E.194, T.196, G.197, S.198, C.199, L.218, S.220, I.221, T.222, C.257, G.258, T.259 Ligands: CL.26 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:L.218 Hydrogen bonds: E:K.160, E:K.160, E:Y.165, E:S.220, E:I.221, E:T.222, E:T.259, E:T.259 Water bridges: E:R.63, E:R.63 Salt bridges: E:H.60, E:R.63 PMP.31: 18 residues within 4Å: Chain F: H.60, R.63, R.149, K.160, Y.165, E.194, T.196, G.197, S.198, C.199, L.218, S.220, I.221, T.222, C.257, G.258, T.259 Ligands: CL.32 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:L.218 Hydrogen bonds: F:K.160, F:K.160, F:Y.165, F:S.220, F:I.221, F:T.222, F:T.259, F:T.259 Water bridges: F:R.63, F:R.63 Salt bridges: F:H.60, F:R.63

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

CL.2: 4 residues within 4Å: Chain A: Y.100, T.259, H.260 Ligands: PMP.1 Ligand excluded by PLIP CL.3: 3 residues within 4Å: Chain A: P.7, Y.95, P.129 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: S.268, R.271 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: I.227, H.228, R.231 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: R.231, E.237, V.238 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain B: Y.100, T.259, H.260 Ligands: PMP.7 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: P.7, Y.95, P.129 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: S.268, R.271 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: I.227, H.228, R.231 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: R.231, E.237, V.238 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: Y.100, T.259, H.260 Ligands: PMP.13 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: P.7, Y.95, P.129 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain C: S.268, R.271 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain C: I.227, H.228, R.231 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain C: R.231, E.237, V.238 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain D: Y.100, T.259, H.260 Ligands: PMP.19 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain D: P.7, Y.95, P.129 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain D: S.268, R.271 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain D: I.227, H.228, R.231 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain D: R.231, E.237, V.238 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain E: Y.100, T.259, H.260 Ligands: PMP.25 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain E: P.7, Y.95, P.129 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain E: S.268, R.271 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain E: I.227, H.228, R.231 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain E: R.231, E.237, V.238 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain F: Y.100, T.259, H.260 Ligands: PMP.31 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain F: P.7, Y.95, P.129 Ligand excluded by PLIP CL.34: 2 residues within 4Å: Chain F: S.268, R.271 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain F: I.227, H.228, R.231 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain F: R.231, E.237, V.238 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bezsudnova, E.Y. et al., Biochemical and structural insights into PLP fold type IV transaminase from Thermobaculum terrenum. Biochimie (2018)

Release Date

2019-01-02

Peptides

Branched-chain-amino-acid aminotransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Branched-chain-amino-acid aminotransferase

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