SMTL ID : 7vno.1

Structure of aminotransferase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

4 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)(Covalent)

PLP.1: 14 residues within 4Å: Chain A: S.123, G.124, T.125, N.128, F.151, H.152, G.153, E.231, D.264, V.266, Q.267, K.293 Chain B: N.320, T.321 19 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:F.151, A:E.231, A:V.266 Hydrogen bonds: A:S.123, A:G.124, A:T.125, A:N.128, A:Q.267, B:T.321, B:T.321, B:T.321 Water bridges: A:S.123, A:F.151, A:E.231, A:K.293, B:N.122, B:F.322 Salt bridges: A:K.293 pi-Stacking: A:F.151 PLP.5: 15 residues within 4Å: Chain A: N.320, T.321, F.322 Chain B: S.123, G.124, T.125, N.128, F.151, H.152, G.153, E.231, D.264, V.266, Q.267, K.293 18 PLIP interactions: 13 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:F.151, B:E.231, B:V.266 Hydrogen bonds: B:G.124, B:T.125, B:Q.267, A:T.321, A:T.321, A:T.321 Water bridges: B:S.123, B:T.125, B:T.125, B:F.151, B:E.231, A:N.122, A:F.322 Salt bridges: B:K.293 pi-Stacking: B:F.151 PLP.8: 14 residues within 4Å: Chain C: S.123, G.124, T.125, N.128, F.151, H.152, G.153, E.231, D.264, V.266, Q.267, K.293 Chain D: N.320, T.321 20 PLIP interactions: 5 interactions with chain D, 15 interactions with chain C Hydrogen bonds: D:T.321, D:T.321, D:T.321, C:S.123, C:G.124, C:T.125, C:N.128, C:Q.267 Water bridges: D:N.122, D:F.322, C:S.123, C:T.125, C:F.151, C:E.231, C:K.293 Hydrophobic interactions: C:F.151, C:E.231, C:V.266 Salt bridges: C:K.293 pi-Stacking: C:F.151 PLP.12: 15 residues within 4Å: Chain C: N.320, T.321, F.322 Chain D: S.123, G.124, T.125, N.128, F.151, H.152, G.153, E.231, D.264, V.266, Q.267, K.293 17 PLIP interactions: 13 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:F.151, D:E.231, D:V.266 Hydrogen bonds: D:G.124, D:T.125, D:Q.267, D:K.293, C:T.321, C:T.321 Water bridges: D:S.123, D:T.125, D:F.151, D:E.231, C:N.122, C:F.322 Salt bridges: D:K.293 pi-Stacking: D:F.151

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: Y.197, R.355, E.359, V.371, R.372 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.355, A:R.355, A:V.371 Water bridges: A:K.362, A:K.362 GOL.6: 5 residues within 4Å: Chain B: Y.197, R.355, E.359, V.371, R.372 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.355, B:R.355, B:E.359 Water bridges: B:K.362, B:K.362 GOL.9: 5 residues within 4Å: Chain C: Y.197, R.355, E.359, V.371, R.372 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.355, C:R.355, C:V.371 Water bridges: C:K.362, C:K.362 GOL.13: 5 residues within 4Å: Chain D: Y.197, R.355, E.359, V.371, R.372 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.355, D:R.355, D:E.359 Water bridges: D:K.362, D:K.362

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

EDO.3: 5 residues within 4Å: Chain A: E.351, R.355, G.373, L.374, W.378 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.355, A:G.373 EDO.4: 6 residues within 4Å: Chain A: G.153, R.154, M.159, T.162, Q.168, R.169 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.169 Water bridges: A:S.164 EDO.7: 5 residues within 4Å: Chain B: E.351, R.355, G.373, L.374, W.378 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.355, B:G.373 EDO.10: 5 residues within 4Å: Chain C: E.351, R.355, G.373, L.374, W.378 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.355, C:G.373 EDO.11: 6 residues within 4Å: Chain C: G.153, R.154, M.159, T.162, Q.168, R.169 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.162, C:R.169 Water bridges: C:S.164 EDO.14: 5 residues within 4Å: Chain D: E.351, R.355, G.373, L.374, W.378 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.355, D:G.373

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kawakami, R. et al., Crystal structure of a novel type of ornithine delta-aminotransferase from the hyperthermophilic archaeon Pyrococcus horikoshii. Int.J.Biol.Macromol. (2022)

Release Date

2022-03-30

Peptides

454aa long hypothetical 4-aminobutyrate aminotransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

454aa long hypothetical 4-aminobutyrate aminotransferase

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