SMTL ID : 4cog.1 (1 other biounit)

Crystal structure of kynurenine formamidase from Burkholderia cenocepacia

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: D.56, H.162, E.174 Ligands: CD.2, GOL.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.56, A:H.162, A:E.174, A:E.174 ZN.11: 5 residues within 4Å: Chain B: D.56, H.162, E.174 Ligands: CD.12, GOL.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.56, B:H.162, B:E.174, B:E.174

2 x CD: CADMIUM ION(Non-covalent)

CD.2: 6 residues within 4Å: Chain A: H.50, H.54, D.56, E.174 Ligands: ZN.1, GOL.6 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.50, A:H.54, A:D.56, A:E.174 CD.12: 6 residues within 4Å: Chain B: H.50, H.54, D.56, E.174 Ligands: ZN.11, GOL.16 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.50, B:H.54, B:D.56, B:E.174

4 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 1 residues within 4Å: Chain A: H.139 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:H.139, H2O.8, H2O.9, H2O.9, H2O.11 MG.4: 2 residues within 4Å: Chain A: D.62, D.64 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.62, A:D.64, H2O.6, H2O.6, H2O.6 MG.13: 2 residues within 4Å: Chain B: D.62, D.64 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.62, B:D.64, H2O.15, H2O.15, H2O.15, H2O.16 MG.14: 1 residues within 4Å: Chain B: H.139 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.139, H2O.19, H2O.19, H2O.19, H2O.21

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 8 residues within 4Å: Chain A: W.20, D.23, H.50, H.60 Chain B: W.32, V.40, V.42 Ligands: GOL.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.23, A:H.60 Water bridges: A:W.20 GOL.6: 13 residues within 4Å: Chain A: W.20, H.50, H.54, D.56, H.60, P.149, S.150, M.159, H.162, E.174 Ligands: ZN.1, CD.2, GOL.5 No protein-ligand interaction detected (PLIP) GOL.7: 9 residues within 4Å: Chain A: P.11, G.52, Y.113, A.116, A.117, D.147, T.148, G.175, I.176 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.117, A:A.117, A:D.147 Water bridges: A:G.52, A:G.52, A:Y.113 GOL.15: 8 residues within 4Å: Chain A: W.32, V.40, V.42 Chain B: W.20, D.23, H.50, H.60 Ligands: GOL.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.23 Water bridges: B:S.48 GOL.16: 13 residues within 4Å: Chain B: W.20, H.50, H.54, D.56, H.60, P.149, S.150, M.159, H.162, E.174 Ligands: ZN.11, CD.12, GOL.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.162 Water bridges: B:H.50 GOL.17: 9 residues within 4Å: Chain B: P.11, G.52, Y.113, A.116, A.117, D.147, T.148, G.175, I.176 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:A.117, B:G.175 Water bridges: B:G.52, B:G.52, B:Y.113, B:Y.113

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

EDO.8: 5 residues within 4Å: Chain A: Y.113, R.115, A.116, A.117, D.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.115, A:D.122 EDO.9: 2 residues within 4Å: Chain A: R.81, D.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.185 Water bridges: A:R.81, A:R.81 EDO.10: 5 residues within 4Å: Chain A: I.86, G.87, T.112, Y.113, A.114 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.114 Water bridges: A:R.115 EDO.18: 2 residues within 4Å: Chain B: P.183, G.184 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.185 EDO.19: 3 residues within 4Å: Chain B: Y.113, R.115, A.116 1 PLIP interactions: 1 interactions with chain B Water bridges: B:V.118 EDO.20: 1 residues within 4Å: Chain B: I.86 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:I.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Diaz-Saez, L. et al., Structure of Bacterial Kynurenine Formamidase Reveals a Crowded Binuclear-Zinc Catalytic Site Primed to Generate a Potent Nucleophile. Biochem.J. (2014)

Release Date

2014-04-02

Peptides

KYNURENINE FORMAMIDASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

KYNURENINE FORMAMIDASE

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