SMTL ID : 5i5y.1

X-RAY CRYSTAL STRUCTURE AT 1.81A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH AN ARYL ACETATE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.81 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: 68D.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:K.206, A:L.270, A:L.270 Hydrogen bonds: A:Y.211, A:V.273, A:V.274, A:T.317 Water bridges: A:G.81, A:R.103, A:R.275, A:T.317, A:T.317 Salt bridges: A:R.103, A:K.206 PLP.7: 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: 68D.8 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:K.206, B:L.270, B:L.270 Hydrogen bonds: B:Y.211, B:V.273, B:V.274, B:T.317 Water bridges: B:R.103, B:R.103, B:R.275, B:T.317, B:T.317 Salt bridges: B:R.103, B:K.206

2 x 68D: {2-[(5-methyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-6-carbonyl)amino]phenyl}acetic acid(Non-covalent)

68D.2: 16 residues within 4Å: Chain A: F.34, F.79, K.83, Y.145, R.147, Y.177, K.206, Y.211, T.244, G.316, T.317, A.318 Chain B: Y.74, V.159 Ligands: PLP.1, EDO.4 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.34, A:F.79, A:F.79, A:Y.145, A:Y.211, A:T.244, A:A.318, B:Y.74, B:V.159 Hydrogen bonds: A:K.83, A:A.318 Water bridges: A:K.83, A:Y.145, A:G.175, A:T.244, A:T.244, A:T.244, A:T.244, A:G.316, A:Q.320 pi-Stacking: A:F.34 68D.8: 15 residues within 4Å: Chain A: Y.74, V.159 Chain B: F.34, F.79, K.83, Y.145, R.147, Y.177, K.206, Y.211, T.244, G.316, T.317, A.318 Ligands: PLP.7 20 PLIP interactions: 2 interactions with chain A, 18 interactions with chain B Hydrophobic interactions: A:Y.74, A:V.159, B:F.34, B:F.79, B:F.79, B:Y.145, B:Y.211, B:T.244, B:A.318 Hydrogen bonds: B:K.83, B:A.318 Water bridges: B:K.83, B:Y.145, B:G.175, B:G.175, B:G.175, B:T.244, B:T.244, B:T.244 pi-Stacking: B:F.34

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.9: 3 residues within 4Å: Chain B: K.83, A.318, Q.320 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: N.204, P.271 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: R.96, W.98 Ligand excluded by PLIP

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

EDO.4: 7 residues within 4Å: Chain A: L.32, V.33, F.34, G.175, A.176, Y.177 Ligands: 68D.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.177 Water bridges: A:F.34 EDO.5: 5 residues within 4Å: Chain A: Y.250, R.310, E.344, L.345, R.348 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.250, A:R.310, A:E.344, A:R.348 Water bridges: A:R.310 EDO.6: 6 residues within 4Å: Chain A: M.44, E.46, R.56, L.63, T.64, L.166 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.46, A:E.46, A:R.56, A:T.64, A:T.64 Water bridges: A:Q.58, A:T.64 EDO.12: 3 residues within 4Å: Chain B: L.119, E.120, E.123 4 PLIP interactions: 4 interactions with chain B Water bridges: B:A.11, B:A.12, B:E.120, B:E.120 EDO.13: 5 residues within 4Å: Chain B: W.98, M.101, D.102, K.118, L.119 No protein-ligand interaction detected (PLIP) EDO.14: 5 residues within 4Å: Chain B: E.46, R.56, L.63, T.64, L.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.46, B:R.56, B:T.64 Water bridges: B:Q.58 EDO.15: 5 residues within 4Å: Chain B: K.88, D.89, Y.358, G.359, I.360 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.88, B:D.89, B:D.89, B:R.93 EDO.16: 4 residues within 4Å: Chain B: Y.250, E.344, L.345, R.348 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:Y.250, B:R.348, B:R.348 Water bridges: B:Y.250, B:R.310, B:R.310, B:E.344, B:E.344, B:E.344 EDO.17: 6 residues within 4Å: Chain B: L.99, R.103, R.106, P.271, G.272, V.273 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.106 Water bridges: B:R.106, B:Q.276, B:Q.276

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 2 residues within 4Å: Chain B: W.98, E.364 No protein-ligand interaction detected (PLIP)

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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