SMTL ID : 2ej0.1

Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase with Pyridoxamine 5'-phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

6 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PMP.1: 15 residues within 4Å: Chain A: R.59, R.148, K.159, Y.164, E.193, S.195, G.196, E.197, N.198, L.216, G.218, I.219, T.220, G.255, T.256 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.216 Hydrogen bonds: A:Y.164, A:G.196, A:I.219, A:T.220, A:T.220, A:T.256 Water bridges: A:E.37, A:K.159, A:K.159, A:R.221, A:T.256, A:A.257, A:A.257 Salt bridges: A:R.59 PMP.4: 14 residues within 4Å: Chain B: R.59, R.148, Y.164, E.193, S.195, G.196, E.197, N.198, L.216, G.218, I.219, T.220, G.255, T.256 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.216 Hydrogen bonds: B:Y.164, B:Y.164, B:G.196, B:I.219, B:T.220, B:T.220, B:T.256, B:T.256 Water bridges: B:E.37, B:R.59, B:Y.95, B:K.159, B:R.221, B:A.257, B:A.257 Salt bridges: B:R.59 PMP.6: 15 residues within 4Å: Chain C: R.59, R.148, K.159, Y.164, E.193, S.195, G.196, E.197, N.198, L.216, G.218, I.219, T.220, G.255, T.256 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:L.216 Hydrogen bonds: C:Y.164, C:Y.164, C:G.196, C:I.219, C:T.220, C:T.256, C:T.256 Water bridges: C:E.37, C:R.59, C:Y.95, C:K.159, C:R.221, C:A.257 Salt bridges: C:R.59 PMP.8: 14 residues within 4Å: Chain D: R.59, R.148, Y.164, E.193, S.195, G.196, E.197, N.198, L.216, G.218, I.219, T.220, G.255, T.256 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:L.216 Hydrogen bonds: D:Y.164, D:Y.164, D:G.196, D:I.219, D:T.220, D:T.256, D:T.256 Water bridges: D:E.37, D:R.59, D:K.159, D:K.159, D:R.221, D:A.257, D:A.257 Salt bridges: D:R.59 PMP.11: 15 residues within 4Å: Chain E: R.59, R.148, K.159, Y.164, E.193, S.195, G.196, E.197, N.198, L.216, G.218, I.219, T.220, G.255, T.256 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:L.216 Hydrogen bonds: E:Y.164, E:Y.164, E:G.196, E:I.219, E:T.220, E:T.256 Water bridges: E:E.37, E:K.159, E:K.159, E:R.221, E:T.256, E:A.257, E:A.257 Salt bridges: E:R.59 PMP.13: 15 residues within 4Å: Chain F: R.59, R.148, K.159, Y.164, E.193, S.195, G.196, E.197, N.198, L.216, G.218, I.219, T.220, G.255, T.256 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:L.216 Hydrogen bonds: F:Y.164, F:G.196, F:I.219, F:T.220, F:T.220, F:T.256 Water bridges: F:E.37, F:K.159, F:K.159, F:R.221, F:T.256, F:A.257 Salt bridges: F:R.59

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

MPD.2: 8 residues within 4Å: Chain A: R.52, E.55, E.217, G.218, I.219, D.222 Chain C: R.203, D.204 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain A Hydrogen bonds: C:D.204, A:R.52 Water bridges: C:D.204 Hydrophobic interactions: A:E.55, A:E.217, A:I.219, A:D.222 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.5: 8 residues within 4Å: Chain A: R.203, D.204 Chain B: R.52, E.55, E.217, G.218, I.219, D.222 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:E.55 Hydrogen bonds: B:E.55, A:R.203 Water bridges: A:R.203, A:R.203 MPD.7: 8 residues within 4Å: Chain B: R.203, D.204 Chain C: R.52, E.55, E.217, G.218, I.219, D.222 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:E.217 Hydrogen bonds: C:E.55, B:R.203 Water bridges: B:R.203, B:R.203 MPD.9: 7 residues within 4Å: Chain B: L.107, G.108 Chain D: Y.95, R.97, W.124, W.126, A.257 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:Y.95, D:W.126 Water bridges: D:Y.95, D:Y.95, B:L.107, B:V.109 MPD.10: 8 residues within 4Å: Chain D: R.52, E.55, E.217, G.218, I.219, D.222 Chain F: R.203, D.204 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:E.55, D:I.219, D:D.222 Hydrogen bonds: D:R.52, F:D.204 Water bridges: F:R.203 MPD.12: 8 residues within 4Å: Chain D: R.203, D.204 Chain E: R.52, E.55, E.217, G.218, I.219, D.222 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain D Hydrophobic interactions: E:E.55, E:E.217, E:I.219, E:D.222 Hydrogen bonds: E:R.52, D:D.204 Water bridges: D:R.203 MPD.14: 3 residues within 4Å: Chain F: D.230, R.295, E.297 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:D.230, F:E.297 Hydrogen bonds: F:R.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goto, M., Crystal Structure of T.th.HB8 Branched-Chain Amino Acid Aminotransferase with Pyridoxamine 5'-phosphate. 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
D

E
E

F
F

Branched-chain amino acid aminotransferase

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