SMTL ID : 1ohl.1

YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE PUTATIVE CYCLIC REACTION INTERMEDIATE COMPLEX

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-octamer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.133, C.135, C.143 Ligands: PBG.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.133, A:C.135, A:C.143 ZN.4: 4 residues within 4Å: Chain B: C.133, C.135, C.143 Ligands: PBG.6 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.133, B:C.135, B:C.143 ZN.7: 4 residues within 4Å: Chain C: C.133, C.135, C.143 Ligands: PBG.9 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.133, C:C.135, C:C.143 ZN.10: 4 residues within 4Å: Chain D: C.133, C.135, C.143 Ligands: PBG.12 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.133, D:C.135, D:C.143 ZN.13: 4 residues within 4Å: Chain E: C.133, C.135, C.143 Ligands: PBG.15 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.133, E:C.135, E:C.143 ZN.16: 4 residues within 4Å: Chain F: C.133, C.135, C.143 Ligands: PBG.18 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.133, F:C.135, F:C.143 ZN.19: 4 residues within 4Å: Chain G: C.133, C.135, C.143 Ligands: PBG.21 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.133, G:C.135, G:C.143 ZN.22: 4 residues within 4Å: Chain H: C.133, C.135, C.143 Ligands: PBG.24 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.133, H:C.135, H:C.143

8 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.2: 3 residues within 4Å: Chain A: R.220, D.221, C.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.221, A:D.221 BME.5: 3 residues within 4Å: Chain B: R.220, D.221, C.224 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.221, B:D.221 BME.8: 3 residues within 4Å: Chain C: R.220, D.221, C.224 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.221, C:D.221 BME.11: 3 residues within 4Å: Chain D: R.220, D.221, C.224 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.221 BME.14: 3 residues within 4Å: Chain E: R.220, D.221, C.224 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.221 BME.17: 3 residues within 4Å: Chain F: R.220, D.221, C.224 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:D.221, F:D.221 BME.20: 3 residues within 4Å: Chain G: R.220, D.221, C.224 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.221 BME.23: 3 residues within 4Å: Chain H: R.220, D.221, C.224 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:D.221

8 x PBG: 3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC ACID(Covalent)

PBG.3: 18 residues within 4Å: Chain A: F.89, D.131, C.133, C.135, C.143, S.179, K.210, Y.216, F.219, R.220, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 Ligands: ZN.1 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:F.219, A:F.219, A:K.263, A:Y.287, A:V.289 Hydrogen bonds: A:S.179, A:S.179, A:K.210, A:Y.216, A:Q.236, A:Y.287, A:S.290, A:Y.329 Salt bridges: A:K.210, A:R.220, A:R.232, A:K.263, A:K.263 pi-Stacking: A:F.219 pi-Cation interactions: A:K.210 PBG.6: 18 residues within 4Å: Chain B: F.89, D.131, C.133, C.135, C.143, S.179, K.210, Y.216, F.219, R.220, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 Ligands: ZN.4 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.219, B:F.219, B:K.263, B:Y.287, B:V.289 Hydrogen bonds: B:S.179, B:S.179, B:K.210, B:Y.216, B:Q.236, B:Y.287, B:S.290, B:Y.329 Salt bridges: B:K.210, B:R.220, B:R.232, B:K.263, B:K.263 pi-Stacking: B:F.219 pi-Cation interactions: B:K.210 PBG.9: 18 residues within 4Å: Chain C: F.89, D.131, C.133, C.135, C.143, S.179, K.210, Y.216, F.219, R.220, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 Ligands: ZN.7 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:F.219, C:F.219, C:K.263, C:Y.287, C:V.289 Hydrogen bonds: C:S.179, C:S.179, C:K.210, C:Y.216, C:Q.236, C:Y.287, C:S.290, C:Y.329 Salt bridges: C:K.210, C:R.220, C:R.232, C:K.263, C:K.263 pi-Stacking: C:F.219 pi-Cation interactions: C:K.210 PBG.12: 18 residues within 4Å: Chain D: F.89, D.131, C.133, C.135, C.143, S.179, K.210, Y.216, F.219, R.220, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 Ligands: ZN.10 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:F.219, D:F.219, D:K.263, D:Y.287, D:V.289 Hydrogen bonds: D:S.179, D:S.179, D:K.210, D:Y.216, D:Q.236, D:S.290 Salt bridges: D:K.210, D:R.220, D:R.232, D:K.263, D:K.263 pi-Stacking: D:F.219 pi-Cation interactions: D:K.210 PBG.15: 18 residues within 4Å: Chain E: F.89, D.131, C.133, C.135, C.143, S.179, K.210, Y.216, F.219, R.220, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 Ligands: ZN.13 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:F.219, E:F.219, E:K.263, E:Y.287, E:V.289 Hydrogen bonds: E:S.179, E:S.179, E:K.210, E:Y.216, E:Q.236, E:S.290 Salt bridges: E:K.210, E:R.220, E:R.232, E:K.263, E:K.263 pi-Stacking: E:F.219 pi-Cation interactions: E:K.210 PBG.18: 18 residues within 4Å: Chain F: F.89, D.131, C.133, C.135, C.143, S.179, K.210, Y.216, F.219, R.220, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 Ligands: ZN.16 20 PLIP interactions: 20 interactions with chain F Hydrophobic interactions: F:F.219, F:F.219, F:K.263, F:Y.287, F:V.289 Hydrogen bonds: F:S.179, F:S.179, F:K.210, F:Y.216, F:Q.236, F:Y.287, F:S.290, F:Y.329 Salt bridges: F:K.210, F:R.220, F:R.232, F:K.263, F:K.263 pi-Stacking: F:F.219 pi-Cation interactions: F:K.210 PBG.21: 18 residues within 4Å: Chain G: F.89, D.131, C.133, C.135, C.143, S.179, K.210, Y.216, F.219, R.220, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 Ligands: ZN.19 18 PLIP interactions: 18 interactions with chain G Hydrophobic interactions: G:F.219, G:F.219, G:K.263, G:Y.287, G:V.289 Hydrogen bonds: G:S.179, G:S.179, G:K.210, G:Y.216, G:Q.236, G:S.290 Salt bridges: G:K.210, G:R.220, G:R.232, G:K.263, G:K.263 pi-Stacking: G:F.219 pi-Cation interactions: G:K.210 PBG.24: 18 residues within 4Å: Chain H: F.89, D.131, C.133, C.135, C.143, S.179, K.210, Y.216, F.219, R.220, R.232, Q.236, K.263, Y.287, V.289, S.290, Y.329 Ligands: ZN.22 18 PLIP interactions: 18 interactions with chain H Hydrophobic interactions: H:F.219, H:F.219, H:K.263, H:Y.287, H:V.289 Hydrogen bonds: H:S.179, H:S.179, H:K.210, H:Y.216, H:Q.236, H:S.290 Salt bridges: H:K.210, H:R.220, H:R.232, H:K.263, H:K.263 pi-Stacking: H:F.219 pi-Cation interactions: H:K.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Erskine, P.T. et al., X-Ray Structure of a Putative Reaction Intermediateof 5-Aminolaevulinic Acid Dehydratase. Biochem.J. (2003)

Release Date

2003-06-02

Peptides

DELTA-AMINOLEVULINIC 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

DELTA-AMINOLEVULINIC ACID DEHYDRATASE

Related Entries With Identical Sequence