SMTL ID : 5i5u.1

X-RAY CRYSTAL STRUCTURE AT 2.40A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A TETRAHYDRONAPHTHALENYL COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 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: 67Y.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:K.206, A:Y.211, A:L.270, A:L.270 Hydrogen bonds: 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.8: 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: 67Y.9 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:K.206, B:L.270, B:L.270 Hydrogen bonds: 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 67Y: 2-hydroxy-N-[(1R)-1,2,3,4-tetrahydronaphthalen-1-yl]acetamide(Non-covalent)

67Y.2: 15 residues within 4Å: Chain A: F.34, F.79, Y.177, K.206, Y.211, T.244, M.245, G.316, T.317, A.318, C.319 Chain B: Y.74, L.157, V.159 Ligands: PLP.1 15 PLIP interactions: 2 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:Y.74, B:V.159, A:F.34, A:F.79, A:Y.177, A:Y.211, A:Y.211, A:T.244, A:A.318 Hydrogen bonds: A:T.244, A:T.244, A:A.318, A:C.319 Water bridges: A:Y.145 pi-Cation interactions: A:R.147 67Y.9: 15 residues within 4Å: Chain A: Y.74, L.157, V.159 Chain B: F.34, F.79, Y.177, K.206, Y.211, T.244, M.245, G.316, T.317, A.318, C.319 Ligands: PLP.8 16 PLIP interactions: 14 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.34, B:F.34, B:F.79, B:F.79, B:Y.177, B:Y.211, B:T.244, B:A.318, A:Y.74, A:V.159 Hydrogen bonds: B:T.244, B:T.244, B:T.317, B:A.318, B:C.319 pi-Cation interactions: B:R.147

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

CL.3: 1 residues within 4Å: Chain A: N.204 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain B: L.265 Ligand excluded by PLIP

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

EDO.4: 5 residues within 4Å: Chain A: Y.250, F.288, R.310, L.345, R.348 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.250, A:R.310, A:R.348 Water bridges: A:E.344 EDO.5: 4 residues within 4Å: Chain A: V.199, Y.233, P.235 Chain B: W.198 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.233 Water bridges: A:G.234 EDO.6: 4 residues within 4Å: Chain A: N.204, L.265, N.266, G.267 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.266 EDO.7: 2 residues within 4Å: Chain A: E.254, R.302 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.254, A:R.302 EDO.12: 6 residues within 4Å: Chain B: D.280, M.281, T.284, E.352, H.363, W.365 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.280, B:E.352, B:H.363 Water bridges: B:D.280, B:T.284 EDO.13: 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.344 EDO.14: 4 residues within 4Å: Chain B: E.46, L.63, T.64, L.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.64 Water bridges: B:T.64, B:T.64, B:T.64

1 x GOL: GLYCEROL(Non-functional Binders)

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

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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