SMTL ID : 1gjp.1

SCHIFF-BASE COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE WITH 4-OXOSEBACIC ACID

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-octamer

Ligands

8 x 4OX: 4-OXODECANEDIOIC ACID(Covalent)

4OX.1: 13 residues within 4Å: Chain A: D.131, S.179, Y.207, K.210, Y.216, F.219, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.207, A:F.219, A:F.219, A:K.263, A:Y.287, A:Y.287 Hydrogen bonds: A:Q.236, A:Q.236, A:Y.287, A:S.290, A:Y.329 Water bridges: A:R.232, A:R.232 Salt bridges: A:K.210, A:R.232, A:K.263, A:K.263 4OX.3: 13 residues within 4Å: Chain B: D.131, S.179, Y.207, K.210, Y.216, F.219, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:Y.207, B:F.219, B:F.219, B:K.263, B:Y.287, B:Y.287 Hydrogen bonds: B:Q.236, B:Q.236, B:Y.287, B:S.290, B:Y.329 Water bridges: B:R.232, B:R.232 Salt bridges: B:K.210, B:R.232, B:K.263, B:K.263 4OX.5: 13 residues within 4Å: Chain C: D.131, S.179, Y.207, K.210, Y.216, F.219, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.207, C:F.219, C:F.219, C:K.263, C:Y.287, C:Y.287 Hydrogen bonds: C:Q.236, C:Q.236, C:Y.287, C:S.290, C:Y.329 Water bridges: C:R.232, C:R.232 Salt bridges: C:K.210, C:R.232, C:K.263, C:K.263 4OX.7: 13 residues within 4Å: Chain D: D.131, S.179, Y.207, K.210, Y.216, F.219, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:Y.207, D:F.219, D:F.219, D:K.263, D:Y.287, D:Y.287 Hydrogen bonds: D:Q.236, D:Q.236, D:S.290 Water bridges: D:R.232, D:R.232 Salt bridges: D:K.210, D:R.232, D:K.263, D:K.263 4OX.9: 13 residues within 4Å: Chain E: D.131, S.179, Y.207, K.210, Y.216, F.219, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:Y.207, E:F.219, E:F.219, E:K.263, E:Y.287, E:Y.287 Hydrogen bonds: E:Q.236, E:Q.236, E:S.290 Water bridges: E:R.232, E:R.232 Salt bridges: E:K.210, E:R.232, E:K.263, E:K.263 4OX.11: 13 residues within 4Å: Chain F: D.131, S.179, Y.207, K.210, Y.216, F.219, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:Y.207, F:F.219, F:F.219, F:K.263, F:Y.287, F:Y.287 Hydrogen bonds: F:Q.236, F:Q.236, F:Y.287, F:S.290, F:Y.329 Water bridges: F:R.232, F:R.232 Salt bridges: F:K.210, F:R.232, F:K.263, F:K.263 4OX.13: 13 residues within 4Å: Chain G: D.131, S.179, Y.207, K.210, Y.216, F.219, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 15 PLIP interactions: 15 interactions with chain G Hydrophobic interactions: G:Y.207, G:F.219, G:F.219, G:K.263, G:Y.287, G:Y.287 Hydrogen bonds: G:Q.236, G:Q.236, G:S.290 Water bridges: G:R.232, G:R.232 Salt bridges: G:K.210, G:R.232, G:K.263, G:K.263 4OX.15: 13 residues within 4Å: Chain H: D.131, S.179, Y.207, K.210, Y.216, F.219, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 15 PLIP interactions: 15 interactions with chain H Hydrophobic interactions: H:Y.207, H:F.219, H:F.219, H:K.263, H:Y.287, H:Y.287 Hydrogen bonds: H:Q.236, H:Q.236, H:S.290 Water bridges: H:R.232, H:R.232 Salt bridges: H:K.210, H:R.232, H:K.263, H:K.263

8 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.133, C.135, C.143, R.232 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.133, A:C.135, A:C.143, H2O.18 ZN.4: 4 residues within 4Å: Chain B: C.133, C.135, C.143, R.232 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.133, B:C.135, B:C.143, H2O.36 ZN.6: 4 residues within 4Å: Chain C: C.133, C.135, C.143, R.232 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.133, C:C.135, C:C.143, H2O.54 ZN.8: 4 residues within 4Å: Chain D: C.133, C.135, C.143, R.232 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.133, D:C.135, D:C.143, H2O.72 ZN.10: 4 residues within 4Å: Chain E: C.133, C.135, C.143, R.232 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:C.133, E:C.135, E:C.143, H2O.90 ZN.12: 4 residues within 4Å: Chain F: C.133, C.135, C.143, R.232 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:C.133, F:C.135, F:C.143, H2O.108 ZN.14: 4 residues within 4Å: Chain G: C.133, C.135, C.143, R.232 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:C.133, G:C.135, G:C.143, H2O.126 ZN.16: 4 residues within 4Å: Chain H: C.133, C.135, C.143, R.232 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:C.133, H:C.135, H:C.143, H2O.144

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Erskine, P.T. et al., The X-Ray Structure of Yeast 5-Aminolaevulinic Acid Dehydratase Complexed with Two Diacid Inhibitors. FEBS Lett. (2001)

Release Date

2001-08-02

Peptides

5-AMINOLAEVULINIC ACID DEHYDRATASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

5-AMINOLAEVULINIC ACID DEHYDRATASE

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