SMTL ID : 5vep.2 (1 other biounit)

MOUSE KYNURENINE AMINOTRANSFERASE III, RE-REFINEMENT OF THE PDB STRUCTURE 3E2F

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-tetramer

Ligands

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

EPE.1: 13 residues within 4Å: Chain A: N.11, W.13, Q.30, G.31, Y.95, Y.119, D.120, N.178, K.240, F.332, F.375, R.389 Chain B: Y.271 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.31, A:Y.95, A:N.178 Water bridges: A:S.10, B:N.268 Salt bridges: A:D.120, A:D.120, A:R.389 EPE.10: 12 residues within 4Å: Chain A: Q.267, Y.271 Chain B: N.11, W.13, Q.30, G.31, Y.95, Y.119, D.120, N.178, F.332, R.389 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.31, B:N.178, A:Q.267, A:N.268 Water bridges: B:Y.209 Salt bridges: B:D.120, B:D.120, B:R.389 EPE.15: 13 residues within 4Å: Chain C: N.11, W.13, Q.30, G.31, Y.95, Y.119, D.120, N.178, K.240, F.332, F.375, R.389 Chain D: Y.271 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:G.31, C:N.178 Water bridges: C:S.10, D:N.268 Salt bridges: C:D.120, C:D.120, C:R.389 EPE.24: 12 residues within 4Å: Chain C: Q.267, Y.271 Chain D: N.11, W.13, Q.30, G.31, Y.95, Y.119, D.120, N.178, F.332, R.389 8 PLIP interactions: 2 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:Q.267, C:N.268, D:G.31, D:Y.95, D:N.178 Salt bridges: D:D.120, D:D.120, D:R.389

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

PEG.2: 3 residues within 4Å: Chain A: L.138, H.383, F.384 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.138 PEG.11: 4 residues within 4Å: Chain B: L.138, R.139, H.383, F.384 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.138 PEG.16: 3 residues within 4Å: Chain C: L.138, H.383, F.384 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.138, C:H.383 PEG.25: 4 residues within 4Å: Chain D: L.138, R.139, H.383, F.384 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:L.138

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.139, S.140, K.141, T.154, F.155, D.156 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.155 GOL.4: 5 residues within 4Å: Chain A: Q.190, A.193, D.194, V.197, P.226 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.190, A:Q.190, A:D.194, A:D.194 GOL.5: 6 residues within 4Å: Chain A: D.200, L.202, E.230, R.231, H.257, L.258 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.200, A:R.231, A:H.257 GOL.6: 6 residues within 4Å: Chain A: K.141, S.151, T.154, T.185, Q.187, E.188 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.141, A:K.141, A:T.185, A:Q.187 GOL.12: 5 residues within 4Å: Chain B: Q.190, A.193, D.194, V.197, P.226 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.226 GOL.13: 4 residues within 4Å: Chain B: I.77, E.210, W.211, H.219 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.210, B:E.210 GOL.17: 6 residues within 4Å: Chain C: R.139, S.140, K.141, T.154, F.155, D.156 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:F.155 GOL.18: 5 residues within 4Å: Chain C: Q.190, A.193, D.194, V.197, P.226 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.190, C:Q.190, C:D.194 GOL.19: 6 residues within 4Å: Chain C: D.200, L.202, E.230, R.231, H.257, L.258 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.200, C:R.231, C:H.257 GOL.20: 6 residues within 4Å: Chain C: K.141, S.151, T.154, T.185, Q.187, E.188 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.141, C:K.141, C:Q.187 GOL.26: 5 residues within 4Å: Chain D: Q.190, A.193, D.194, V.197, P.226 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.194, D:P.226 GOL.27: 4 residues within 4Å: Chain D: I.77, E.210, W.211, H.219 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.210

8 x CA: CALCIUM ION(Non-covalent)

CA.7: 4 residues within 4Å: Chain A: Q.81 Chain C: Q.81, D.83 Ligands: CA.21 No protein-ligand interaction detected (PLIP) CA.8: 3 residues within 4Å: Chain A: S.166, H.199, D.200 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.199, H2O.3, H2O.3, H2O.3 CA.9: 2 residues within 4Å: Chain A: N.1, E.6 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.6, A:E.6 CA.14: 1 residues within 4Å: Chain B: H.199 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.199, H2O.5, H2O.5, H2O.6, H2O.7 CA.21: 4 residues within 4Å: Chain A: Q.81, D.83 Chain C: Q.81 Ligands: CA.7 No protein-ligand interaction detected (PLIP) CA.22: 3 residues within 4Å: Chain C: S.166, H.199, D.200 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:H.199, H2O.9, H2O.9, H2O.9 CA.23: 2 residues within 4Å: Chain C: N.1, E.6 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:E.6, C:E.6 CA.28: 1 residues within 4Å: Chain D: H.199 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:H.199, H2O.11, H2O.11, H2O.12, H2O.13

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Kynurenine--oxoglutarate transaminase 3

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