SMTL ID : 3wx9.1

Crystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with PMP, GLA, 4AD, 2OG, GLU and KYA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.58 Å

Oligo State

homo-dimer

Ligands

2 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Covalent)

PMP.1: 16 residues within 4Å: Chain A: G.148, S.149, Q.150, Y.174, V.223, N.228, D.256, P.258, Y.259, T.286, S.288, K.289, R.296 Chain B: Y.114, L.319 Ligands: G9A.3 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.174, A:V.223 Hydrogen bonds: A:S.149, A:Q.150, A:N.228, A:Y.259, A:T.286, A:S.288, A:S.288, B:Y.114 Salt bridges: A:K.289, A:R.296 pi-Stacking: A:Y.174 PMP.6: 16 residues within 4Å: Chain A: Y.114, L.319 Chain B: G.148, S.149, Q.150, Y.174, V.223, N.228, D.256, P.258, Y.259, T.286, S.288, K.289, R.296 Ligands: G9A.8 13 PLIP interactions: 11 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.174, B:V.223 Hydrogen bonds: B:S.149, B:S.149, B:Q.150, B:N.228, B:S.288, A:Y.114, A:Y.114 Water bridges: B:T.286 Salt bridges: B:K.289, B:R.296 pi-Stacking: B:Y.174

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.2: 12 residues within 4Å: Chain A: Y.135, D.257, P.258, Y.259, G.260, E.261, L.262, Y.283, G.285, T.286, I.290, W.299 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:E.261, A:I.290, A:I.290 Hydrogen bonds: A:G.260, A:E.261, A:L.262, A:T.286 AKG.7: 11 residues within 4Å: Chain B: Y.135, D.257, P.258, G.260, E.261, K.271, Y.283, G.285, T.286, I.290, W.299 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.135 Hydrogen bonds: B:Y.135, B:D.257, B:D.257, B:E.261, B:T.286 Salt bridges: B:K.271

2 x G9A: (2E)-pent-2-enedioic acid(Non-covalent)

G9A.3: 11 residues within 4Å: Chain A: G.84, Y.174, L.175, A.176, N.228, Y.259, M.377, F.378, R.420 Ligands: PMP.1, 3EE.4 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain A Water bridges: E.5, A:Y.174, A:Y.174, A:L.175, A:R.420 Hydrophobic interactions: A:Y.174 Hydrogen bonds: A:A.176 Salt bridges: A:K.289, A:R.420 G9A.8: 13 residues within 4Å: Chain B: R.67, G.84, Y.174, L.175, A.176, N.228, Y.259, K.289, M.377, F.378, R.420 Ligands: PMP.6, 3EE.9 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.174 Hydrogen bonds: B:A.176, B:N.228, B:Y.259, B:Y.259 Water bridges: B:R.67, B:R.67, B:L.175, B:R.420 Salt bridges: B:R.67, B:K.289, B:R.420

2 x 3EE: 4-(2-aminophenyl)-2,4-dioxobutanoic acid(Non-covalent)

3EE.4: 7 residues within 4Å: Chain A: R.67, G.83, G.84, L.85, R.420 Chain B: Y.114 Ligands: G9A.3 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:L.85 Hydrogen bonds: A:R.67, A:G.84, A:R.420, A:R.420 Water bridges: A:A.82 pi-Stacking: B:Y.114 3EE.9: 8 residues within 4Å: Chain A: Y.114, L.319 Chain B: E.74, G.83, G.84, L.85, R.420 Ligands: G9A.8 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.85, A:L.319 Hydrogen bonds: B:G.84, B:R.420 Water bridges: B:E.74, A:G.115 pi-Stacking: A:Y.114

1 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.5: 7 residues within 4Å: Chain A: S.64, V.66, R.67, L.175, V.404, A.408, R.413 6 PLIP interactions: 2 Ligand-Ligand interactions, 4 interactions with chain A Hydrogen bonds: E.5, E.5, A:S.64 Water bridges: A:R.67, A:R.413 Salt bridges: A:R.413

1 x KYA: 4-hydroxyquinoline-2-carboxylic acid(Non-covalent)

KYA.10: 9 residues within 4Å: Chain B: S.64, V.66, R.67, L.175, Q.179, K.390, V.404, A.408, R.413 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:V.66, B:L.175 Hydrogen bonds: B:R.67, B:R.413, B:R.413 Water bridges: B:V.66, B:K.390, B:K.390 Salt bridges: B:K.390, B:R.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okada, K. et al., Crystal structure of Pyrococcus horikoshii kynurenine aminotransferase in complex with PMP, GLA, 4AD, 2OG, GLU and KYA. To be Published

Release Date

2014-09-24

Peptides

Putative uncharacterized protein PH0207: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

Putative uncharacterized protein PH0207

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