SMTL ID : 2eiy.1

Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase Complexed with 4-Methylvaleric Acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-hexamer

Ligands

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

PLP.1: 15 residues within 4Å: Chain A: R.59, R.148, K.159, Y.164, E.193, S.195, G.196, E.197, L.216, G.218, I.219, T.220, G.255, T.256 Ligands: 4MV.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:K.159, A:L.216 Hydrogen bonds: A:Y.164, A:Y.164, A:I.219, A:T.220, A:T.256 Water bridges: A:E.37, A:R.221, A:T.256 Salt bridges: A:R.59, A:K.159 PLP.5: 14 residues within 4Å: Chain B: R.59, R.148, K.159, Y.164, E.193, G.196, E.197, L.216, G.218, I.219, T.220, G.255, T.256 Ligands: 4MV.6 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:K.159, B:L.216 Hydrogen bonds: B:Y.164, B:I.219, B:T.220, B:T.220, B:T.256 Water bridges: B:E.37, B:R.221, B:T.256 Salt bridges: B:R.59, B:K.159 PLP.9: 14 residues within 4Å: Chain C: R.59, R.148, K.159, Y.164, E.193, G.196, E.197, L.216, G.218, I.219, T.220, G.255, T.256 Ligands: 4MV.10 13 PLIP interactions: 13 interactions with chain C Hydrophobic interactions: C:K.159, C:L.216 Hydrogen bonds: C:Y.164, C:Y.164, C:I.219, C:T.220, C:T.256, C:T.256 Water bridges: C:E.37, C:R.59, C:R.221 Salt bridges: C:R.59, C:K.159 PLP.12: 15 residues within 4Å: Chain D: R.59, R.148, K.159, Y.164, E.193, S.195, G.196, E.197, L.216, G.218, I.219, T.220, G.255, T.256 Ligands: 4MV.13 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:K.159, D:L.216 Hydrogen bonds: D:Y.164, D:I.219, D:T.220, D:T.220, D:T.256, D:T.256 Water bridges: D:E.37, D:R.59, D:R.221 Salt bridges: D:R.59, D:K.159 PLP.16: 14 residues within 4Å: Chain E: R.59, R.148, K.159, Y.164, E.193, G.196, E.197, L.216, G.218, I.219, T.220, G.255, T.256 Ligands: 4MV.17 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:K.159, E:L.216 Hydrogen bonds: E:Y.164, E:Y.164, E:I.219, E:T.220, E:T.256, E:T.256 Water bridges: E:E.37, E:R.59, E:R.221 Salt bridges: E:R.59, E:K.159 PLP.20: 14 residues within 4Å: Chain F: R.59, R.148, K.159, Y.164, E.193, G.196, E.197, L.216, G.218, I.219, T.220, G.255, T.256 Ligands: 4MV.21 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:K.159, F:L.216 Hydrogen bonds: F:Y.164, F:I.219, F:T.220, F:T.220, F:T.256 Water bridges: F:E.37, F:R.221, F:T.256 Salt bridges: F:R.59, F:K.159

6 x 4MV: 4-METHYL VALERIC ACID(Non-covalent)

4MV.2: 10 residues within 4Å: Chain A: F.36, G.38, Y.95, R.97, Y.164, G.196, T.256, A.257 Chain F: Y.31 Ligands: PLP.1 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:F.36, A:Y.164, F:Y.31 Hydrogen bonds: A:T.256, A:A.257 Water bridges: A:G.196, A:A.258 4MV.6: 11 residues within 4Å: Chain B: F.36, G.38, Y.95, R.97, Y.164, G.196, T.256, A.257 Chain E: Y.31, V.109 Ligands: PLP.5 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:F.36, B:Y.164, E:Y.31 Hydrogen bonds: B:Y.95, B:T.256, B:A.257 Water bridges: B:A.258 4MV.10: 8 residues within 4Å: Chain C: F.36, G.38, Y.95, G.196, T.256, A.257 Chain D: Y.31 Ligands: PLP.9 9 PLIP interactions: 8 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:F.36, D:Y.31 Hydrogen bonds: C:Y.95, C:Y.95, C:T.256, C:A.257 Water bridges: C:G.38, C:A.258 Salt bridges: C:K.159 4MV.13: 10 residues within 4Å: Chain C: Y.31 Chain D: F.36, G.38, Y.95, R.97, Y.164, G.196, T.256, A.257 Ligands: PLP.12 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.36, D:Y.164, C:Y.31 Hydrogen bonds: D:Y.95, D:T.256, D:A.257 Water bridges: D:G.196, D:A.258 4MV.17: 11 residues within 4Å: Chain B: Y.31, V.109 Chain E: F.36, G.38, Y.95, R.97, Y.164, G.196, T.256, A.257 Ligands: PLP.16 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:F.36, E:Y.164, B:Y.31 Hydrogen bonds: E:Y.95, E:Y.95, E:T.256, E:A.257 Water bridges: E:A.258 4MV.21: 8 residues within 4Å: Chain A: Y.31 Chain F: F.36, G.38, Y.95, G.196, T.256, A.257 Ligands: PLP.20 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:F.36, A:Y.31 Hydrogen bonds: F:Y.95, F:T.256, F:A.257 Water bridges: F:G.38, F:A.258 Salt bridges: F:K.159

10 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 3 residues within 4Å: Chain A: D.230, R.295, E.297 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.230, A:E.297 Hydrogen bonds: A:R.295 MPD.4: 8 residues within 4Å: Chain A: R.52, E.55, E.217, G.218, I.219, D.222 Chain C: R.203, D.204 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:E.217, A:I.219, A:D.222 Hydrogen bonds: A:G.218, C:R.203 Water bridges: A:R.221 MPD.7: 5 residues within 4Å: Chain B: Y.95, W.124, E.125, W.126 Chain E: L.107 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain E Hydrophobic interactions: B:Y.95, B:Y.95, B:W.124 Water bridges: B:G.127, E:L.107 MPD.8: 8 residues within 4Å: Chain A: R.203, D.204 Chain B: R.52, E.55, E.217, G.218, I.219, D.222 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.203 Water bridges: A:R.203, A:R.203 Hydrophobic interactions: B:E.55 MPD.11: 8 residues within 4Å: Chain B: R.203, D.204 Chain C: R.52, E.55, E.217, G.218, I.219, D.222 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:E.217, C:I.219, C:D.222 Hydrogen bonds: C:G.218, B:D.204 Water bridges: C:R.221, C:D.222 MPD.14: 3 residues within 4Å: Chain D: D.230, R.295, E.297 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:D.230, D:E.297 Hydrogen bonds: D:R.295 MPD.15: 8 residues within 4Å: Chain D: R.52, E.55, E.217, G.218, I.219, D.222 Chain F: R.203, D.204 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:E.217, D:I.219, D:D.222 Hydrogen bonds: D:G.218, F:R.203, F:D.204 Water bridges: D:R.221 MPD.18: 5 residues within 4Å: Chain B: L.107 Chain E: Y.95, W.124, E.125, W.126 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:Y.95, E:Y.95, E:W.124 Water bridges: E:G.127, B:L.107 MPD.19: 8 residues within 4Å: Chain D: R.203, D.204 Chain E: R.52, E.55, E.217, G.218, I.219, D.222 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:E.55 Hydrogen bonds: E:E.55, D:R.203 Water bridges: D:R.203, D:R.203 MPD.22: 8 residues within 4Å: Chain E: R.203, D.204 Chain F: R.52, E.55, E.217, G.218, I.219, D.222 7 PLIP interactions: 1 interactions with chain E, 6 interactions with chain F Hydrogen bonds: E:D.204, F:G.218 Hydrophobic interactions: F:E.217, F:I.219, F:D.222 Water bridges: F:R.221, F:D.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goto, M., Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase Complexed with 4-Methylvaleric Acid. To be published

Release Date

2008-03-18

Peptides

Branched-chain amino acid aminotransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Branched-chain amino acid aminotransferase

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