SMTL ID : 5mr0.1

Thermophilic archaeal branched-chain amino acid transaminases from Geoglobus acetivorans and Archaeoglobus fulgidus: biochemical and structural characterisation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

homo-hexamer

Ligands

5 x PXG: 3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID(Non-covalent)

PXG.1: 22 residues within 4Å: Chain A: F.32, H.48, R.51, R.89, R.139, K.150, Y.154, N.157, E.183, S.185, G.186, D.187, N.188, L.206, G.208, I.209, T.210, T.244, G.245, T.246 Chain B: G.100, L.101 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.32, A:L.206 Hydrogen bonds: A:K.150, A:Y.154, A:Y.154, A:G.186, A:I.209, A:T.210, A:T.246, B:L.101 Water bridges: A:R.51, A:G.186, A:T.210, A:R.211, A:T.246, A:A.247, A:A.247 Salt bridges: A:H.48, A:R.51, A:K.150 PXG.6: 21 residues within 4Å: Chain A: G.100, L.101 Chain B: H.48, R.51, R.89, R.139, K.150, Y.154, N.157, E.183, S.185, G.186, D.187, N.188, L.206, G.208, I.209, T.210, T.244, G.245, T.246 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:L.206 Hydrogen bonds: B:K.150, B:Y.154, B:G.186, B:I.209, B:T.210, B:T.210, B:T.246, A:L.101 Water bridges: B:R.51, B:R.211, B:T.246 Salt bridges: B:H.48, B:R.51, B:K.150 PXG.12: 22 residues within 4Å: Chain C: H.48, R.51, R.89, R.139, K.150, Y.154, N.157, E.183, S.185, G.186, D.187, N.188, L.206, G.208, I.209, T.210, T.244, G.245, T.246 Chain D: G.100, L.101 Ligands: PEG.17 18 PLIP interactions: 16 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:L.206, D:L.101 Hydrogen bonds: C:K.150, C:Y.154, C:G.186, C:I.209, C:T.210, C:T.210, C:T.246, D:L.101 Water bridges: C:R.211, C:T.246, C:T.246, C:A.247, C:A.247 Salt bridges: C:H.48, C:R.51, C:K.150 PXG.20: 22 residues within 4Å: Chain C: G.100, L.101 Chain D: F.32, H.48, R.51, R.89, R.139, K.150, Y.154, N.157, E.183, S.185, G.186, D.187, N.188, L.206, G.208, I.209, T.210, T.244, G.245, T.246 20 PLIP interactions: 18 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:F.32, D:L.206 Hydrogen bonds: D:K.150, D:Y.154, D:Y.154, D:G.186, D:G.186, D:I.209, D:T.210, D:T.246, D:T.246, C:L.101 Water bridges: D:R.51, D:T.210, D:R.211, D:A.247, C:D.102 Salt bridges: D:H.48, D:R.51, D:K.150 PXG.23: 22 residues within 4Å: Chain E: F.32, H.48, R.51, R.89, R.139, K.150, Y.154, N.157, E.183, S.185, G.186, D.187, N.188, L.206, G.208, I.209, T.210, T.244, G.245, T.246 Chain F: G.100, L.101 20 PLIP interactions: 18 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:F.32, E:L.206, F:L.101 Hydrogen bonds: E:K.150, E:Y.154, E:Y.154, E:G.186, E:I.209, E:T.210, E:T.210, E:T.246, E:T.246, F:L.101 Water bridges: E:R.51, E:K.150, E:R.211, E:A.247 Salt bridges: E:H.48, E:R.51, E:K.150

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

CL.2: 5 residues within 4Å: Chain A: S.141, A.144 Chain B: N.140, S.141, A.144 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: N.229 Chain C: P.201, I.203 Ligands: TAM.18 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain B: N.229 Chain E: P.201, I.203 Ligands: TAM.11 Ligand excluded by PLIP CL.13: 6 residues within 4Å: Chain C: N.140, S.141, A.144 Chain D: N.140, S.141, A.144 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain C: N.229 Chain F: P.201, I.203 Ligands: TAM.18 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: P.201, I.203 Chain D: N.229 Ligands: TAM.11 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain E: S.141, A.144 Chain F: S.141, A.144 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain D: P.201 Chain E: N.229 Ligands: TAM.11 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain A: P.201, I.203 Chain F: N.229 Ligands: TAM.18 Ligand excluded by PLIP

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

PEG.4: 4 residues within 4Å: Chain A: N.14, K.116 Chain B: F.21, I.96 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.14, A:K.116 PEG.5: 7 residues within 4Å: Chain A: N.165, A.166, K.167, G.168 Chain D: A.166, K.167, G.168 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.166 PEG.8: 3 residues within 4Å: Chain A: F.21 Chain B: E.13, K.116 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:K.116, A:G.97 PEG.9: 6 residues within 4Å: Chain A: Y.87, W.118, A.247 Chain B: D.98, L.99, G.100 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.99, A:Y.87 PEG.10: 3 residues within 4Å: Chain B: Y.5, G.8, F.10 1 PLIP interactions: 1 interactions with chain B Water bridges: B:Y.5 PEG.15: 3 residues within 4Å: Chain C: N.194, G.195, I.269 1 PLIP interactions: 1 interactions with chain C Water bridges: C:G.195 PEG.16: 2 residues within 4Å: Chain C: N.219, R.220 No protein-ligand interaction detected (PLIP) PEG.17: 6 residues within 4Å: Chain C: Y.87, W.118, A.247 Chain D: L.99, G.100 Ligands: PXG.12 3 PLIP interactions: 3 interactions with chain D Water bridges: D:L.99, D:L.99, D:L.101 PEG.22: 5 residues within 4Å: Chain D: Y.5, G.8, F.10, I.73, E.76 No protein-ligand interaction detected (PLIP)

2 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.11: 9 residues within 4Å: Chain B: T.228, N.229 Chain D: T.228, N.229 Chain E: T.228, N.229 Ligands: CL.7, CL.21, CL.25 10 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D, 4 interactions with chain B Hydrogen bonds: E:T.228, E:N.229, E:N.229, D:T.228, D:N.229, D:N.229, B:T.228, B:T.228, B:N.229, B:N.229 TAM.18: 9 residues within 4Å: Chain A: T.228, N.229 Chain C: T.228, N.229 Chain F: T.228, N.229 Ligands: CL.3, CL.14, CL.26 10 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A, 3 interactions with chain F Hydrogen bonds: C:T.228, C:T.228, C:N.229, C:N.229, A:T.228, A:N.229, A:N.229, F:T.228, F:N.229 Water bridges: F:T.228

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

EDO.19: 2 residues within 4Å: Chain C: K.116 Chain D: F.21 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.116, C:K.116

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Isupov, M.N. et al., Thermostable Branched-Chain Amino Acid Transaminases From the ArchaeaGeoglobus acetivoransandArchaeoglobus fulgidus: Biochemical and Structural Characterization. Front Bioeng Biotechnol (2019)

Release Date

2018-01-17

Peptides

Putative branched-chain-amino-acid aminotransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Putative branched-chain-amino-acid aminotransferase

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