SMTL ID : 5ver.1 (1 other biounit)

MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2Z

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.81 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 15 residues within 4Å: Chain A: G.93, A.94, Y.95, Y.119, Y.122, N.174, N.178, D.206, V.208, Y.209, S.237, K.240, K.248 Chain B: Y.57 Ligands: EPE.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.94, A:Y.95, A:N.178, A:Y.209, A:S.237, A:S.237 Salt bridges: A:K.240, A:K.248 pi-Stacking: A:Y.119

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.2: 14 residues within 4Å: Chain A: W.13, Q.30, G.31, Y.119, N.178, K.240, F.332, R.389 Chain B: Y.57, T.58, G.60, Y.271, T.272 Ligands: PLP.1 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:G.31, A:Y.119, A:N.178, B:T.272, B:T.272 Salt bridges: A:K.240, A:R.389 EPE.10: 14 residues within 4Å: Chain A: Y.57, T.58, R.59, G.60, Y.271, T.272 Chain B: W.13, Q.30, G.31, Y.119, N.178, F.332, R.389 Ligands: PMP.9 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.31, B:N.178, A:T.272 Water bridges: B:Y.119, B:K.248 Salt bridges: B:R.389

1 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 5 residues within 4Å: Chain A: P.137, L.138, P.382, H.383, F.384 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.138

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: I.77, E.210, W.211, H.219, K.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.210 GOL.5: 5 residues within 4Å: Chain A: K.141, T.154, T.185, Q.187, E.188 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.141, A:T.154, A:T.185, A:Q.187 GOL.12: 4 residues within 4Å: Chain B: Q.190, D.194, V.197, P.226 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.190 GOL.13: 5 residues within 4Å: Chain B: I.77, E.210, W.211, H.219, K.221 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.210, B:E.210

4 x CA: CALCIUM ION(Non-covalent)

CA.6: 1 residues within 4Å: Chain A: Q.81 No protein-ligand interaction detected (PLIP) CA.7: 2 residues within 4Å: Chain A: H.199, D.200 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.199, H2O.1, H2O.1, H2O.2, H2O.3 CA.8: 2 residues within 4Å: Chain A: N.1, E.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.6 CA.14: 2 residues within 4Å: Chain B: H.199, D.200 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.199, H2O.3, H2O.4, H2O.4, H2O.4

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

PMP.9: 15 residues within 4Å: Chain A: Y.57 Chain B: G.93, A.94, Y.95, Y.119, Y.122, N.174, N.178, D.206, V.208, Y.209, S.237, K.240, K.248 Ligands: EPE.10 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.209 Hydrogen bonds: B:A.94, B:Y.95, B:N.178, B:S.237, B:K.240, B:K.240, A:Y.57 Water bridges: B:K.248, B:K.248 Salt bridges: B:K.240, B:K.248 pi-Stacking: B:Y.119

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 1 residues within 4Å: Chain B: H.383 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wlodawer, A. et al., Detect, correct, retract: How to manage incorrect structural models. FEBS J. (2018)

Release Date

2017-11-29

Peptides

Kynurenine--oxoglutarate transaminase 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Kynurenine--oxoglutarate transaminase 3

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