SMTL ID : 5i5s.1

X-RAY CRYSTAL STRUCTURE AT 2.06A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A BENZISOXAZOLE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 15 residues within 4Å: Chain A: R.103, R.196, K.206, Y.211, E.241, T.244, M.245, N.246, L.270, G.272, V.273, V.274, G.316, T.317 Ligands: NVU.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:K.206, A:L.270, A:L.270 Hydrogen bonds: A:Y.211, A:Y.211, A:V.273, A:V.274, A:T.317, A:T.317 Water bridges: A:R.103, A:R.103, A:R.103, A:R.103, A:R.275 Salt bridges: A:R.103, A:K.206 PLP.12: 15 residues within 4Å: Chain B: R.103, R.196, K.206, Y.211, E.241, T.244, M.245, N.246, L.270, G.272, V.273, V.274, G.316, T.317 Ligands: NVU.13 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:K.206, B:L.270, B:L.270 Hydrogen bonds: B:K.206, B:Y.211, B:Y.211, B:V.273, B:V.274, B:T.317, B:T.317 Water bridges: B:R.103, B:R.103, B:R.103, B:R.103, B:R.275 Salt bridges: B:R.103, B:K.206

2 x NVU: 2-(1,2-benzoxazol-3-yl)ethanoic acid(Non-covalent)

NVU.2: 11 residues within 4Å: Chain A: F.34, F.79, R.147, K.206, T.244, T.317, A.318 Chain B: Y.74, L.157, V.159 Ligands: PLP.1 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.34, A:A.318, B:Y.74, B:V.159 Hydrogen bonds: A:T.244, A:T.244, A:A.318 Water bridges: A:C.319 NVU.13: 13 residues within 4Å: Chain A: Y.74, L.157, V.159 Chain B: F.34, F.79, Y.145, R.147, K.206, T.244, G.316, T.317, A.318 Ligands: PLP.12 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:Y.74, A:V.159, B:F.34, B:A.318 Hydrogen bonds: B:K.206, B:T.317, B:A.318 Water bridges: B:C.319

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

CL.3: 3 residues within 4Å: Chain A: R.96, W.98 Ligands: EDO.10 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: N.204 Ligands: EDO.9 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: R.96, W.98 Ligands: EDO.19 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Chain B: N.204 Ligand excluded by PLIP

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

EDO.5: 4 residues within 4Å: Chain A: Y.250, E.344, L.345, R.348 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.250, A:R.348, A:R.348 Water bridges: A:R.310, A:E.344 EDO.6: 6 residues within 4Å: Chain A: D.280, M.281, T.284, E.352, H.363, W.365 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.280, A:T.284, A:H.363 EDO.7: 3 residues within 4Å: Chain A: E.46, L.63, T.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.46, A:T.64 Water bridges: A:N.62 EDO.8: 4 residues within 4Å: Chain A: P.264, L.265, N.266 Ligands: EDO.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.265 EDO.9: 6 residues within 4Å: Chain A: N.204, L.265, N.266, G.267 Ligands: CL.4, EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.204 EDO.10: 3 residues within 4Å: Chain A: W.98, E.364 Ligands: CL.3 No protein-ligand interaction detected (PLIP) EDO.16: 6 residues within 4Å: Chain B: D.280, M.281, T.284, E.352, H.363, W.365 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.280, B:E.352, B:H.363 Water bridges: B:T.284 EDO.17: 5 residues within 4Å: Chain B: Y.250, R.310, E.344, L.345, R.348 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.250, B:Y.250, B:R.310, B:R.348 EDO.18: 7 residues within 4Å: Chain A: R.110, G.200, G.201, V.202 Chain B: I.195, P.213, V.217 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.195, A:R.110 EDO.19: 2 residues within 4Å: Chain B: W.98 Ligands: CL.14 2 PLIP interactions: 2 interactions with chain B Water bridges: B:W.98, B:W.98

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 4 residues within 4Å: Chain A: G.286, E.287, F.288, R.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.286 Water bridges: A:R.289

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.20: 5 residues within 4Å: Chain B: E.46, R.56, L.63, T.64, L.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.64 Salt bridges: B:E.46

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borthwick, J.A. et al., Structurally Diverse Mitochondrial Branched Chain Aminotransferase (BCATm) Leads with Varying Binding Modes Identified by Fragment Screening. J.Med.Chem. (2016)

Release Date

2016-03-23

Peptides

Branched-chain-amino-acid aminotransferase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Branched-chain-amino-acid aminotransferase, mitochondrial

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