SMTL ID : 5i5t.1

X-RAY CRYSTAL STRUCTURE AT 2.31A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A TETRAHYDROQUINOLINE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 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: 67X.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.206, A:L.270 Hydrogen bonds: A:K.206, A:Y.211, A:V.273, A:V.274, A:T.317, A:T.317 Water bridges: A:N.100, A:R.103, A:R.103, A:R.103, A:R.275 Salt bridges: A:R.103, A:K.206 PLP.10: 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: 67X.11 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 67X: (3R)-3-methyl-1,2,3,4-tetrahydroquinoline-8-sulfonamide(Non-covalent)

67X.2: 16 residues within 4Å: Chain A: F.34, F.79, R.147, Y.177, K.206, Y.211, T.244, M.245, G.316, T.317, A.318 Chain B: Y.74, L.157, G.158, V.159 Ligands: PLP.1 10 PLIP interactions: 9 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.34, A:F.79, A:Y.177, A:Y.211, B:V.159 Hydrogen bonds: A:T.244, A:T.244, A:T.317, A:A.318 Water bridges: A:Y.145 67X.11: 12 residues within 4Å: Chain A: Y.74, L.157, G.158, V.159 Chain B: F.34, F.79, K.206, T.244, G.316, T.317, A.318 Ligands: PLP.10 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.34, B:F.79, A:V.159 Hydrogen bonds: B:T.244, B:T.244, B:T.317, B:A.318 Water bridges: B:T.244

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

CL.3: 2 residues within 4Å: Chain A: N.204, P.271 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: R.96, W.98 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: N.204, L.265 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: R.96, W.98 Ligand excluded by PLIP

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

EDO.5: 5 residues within 4Å: Chain A: Y.250, R.310, E.344, L.345, R.348 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.250, A:R.310, A:R.348, A:R.348 EDO.6: 3 residues within 4Å: Chain A: H.253, R.293, Q.299 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.253 Water bridges: A:Q.299 EDO.7: 4 residues within 4Å: Chain A: E.46, L.63, T.64, L.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.64 EDO.8: 3 residues within 4Å: Chain A: P.264, L.265, N.266 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.265 EDO.14: 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:D.280 EDO.15: 7 residues within 4Å: Chain B: Y.250, E.287, F.288, R.310, E.344, L.345, R.348 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.250, B:E.287, B:R.310, B:R.348 Water bridges: B:R.310, B:E.311 EDO.16: 4 residues within 4Å: Chain B: E.46, L.63, T.64, L.166 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.46, B:T.64 Water bridges: B:T.64

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

DMS.9: 4 residues within 4Å: Chain A: D.280, M.281, T.284, H.363 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:W.365

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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