SMTL ID : 1w1z.1

Structure of the plant like 5-Aminolaevulinic Acid Dehydratase from Chlorobium vibrioforme

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-octamer

Ligands

8 x SHF: LAEVULINIC ACID(Covalent)

SHF.1: 8 residues within 4Å: Chain A: F.84, Y.206, F.209, K.253, Y.276, V.278, S.279, Y.318 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.84, A:F.209, A:F.209, A:K.253, A:Y.276 Hydrogen bonds: A:Y.276, A:Y.276, A:S.279, A:Y.318 Salt bridges: A:K.253 SHF.3: 8 residues within 4Å: Chain B: F.84, Y.206, F.209, K.253, Y.276, V.278, S.279, Y.318 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.84, B:Y.206, B:F.209, B:F.209, B:K.253, B:Y.276, B:Y.276 Hydrogen bonds: B:S.279 Salt bridges: B:K.253 SHF.5: 8 residues within 4Å: Chain C: F.84, Y.206, F.209, K.253, Y.276, V.278, S.279, Y.318 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.84, C:F.209, C:F.209, C:K.253, C:Y.276 Hydrogen bonds: C:Y.276, C:Y.276, C:S.279, C:Y.318 Salt bridges: C:K.253 SHF.7: 8 residues within 4Å: Chain D: F.84, Y.206, F.209, K.253, Y.276, V.278, S.279, Y.318 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.84, D:Y.206, D:F.209, D:F.209, D:K.253, D:Y.276, D:Y.276 Hydrogen bonds: D:S.279 Salt bridges: D:K.253 SHF.9: 8 residues within 4Å: Chain E: F.84, Y.206, F.209, K.253, Y.276, V.278, S.279, Y.318 10 PLIP interactions: 10 interactions with chain E Hydrophobic interactions: E:F.84, E:F.209, E:F.209, E:K.253, E:Y.276 Hydrogen bonds: E:Y.276, E:Y.276, E:S.279, E:Y.318 Salt bridges: E:K.253 SHF.11: 8 residues within 4Å: Chain F: F.84, Y.206, F.209, K.253, Y.276, V.278, S.279, Y.318 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:F.84, F:Y.206, F:F.209, F:F.209, F:K.253, F:Y.276, F:Y.276 Hydrogen bonds: F:S.279 Salt bridges: F:K.253 SHF.13: 8 residues within 4Å: Chain G: F.84, Y.206, F.209, K.253, Y.276, V.278, S.279, Y.318 10 PLIP interactions: 10 interactions with chain G Hydrophobic interactions: G:F.84, G:F.209, G:F.209, G:K.253, G:Y.276 Hydrogen bonds: G:Y.276, G:Y.276, G:S.279, G:Y.318 Salt bridges: G:K.253 SHF.15: 8 residues within 4Å: Chain H: F.84, Y.206, F.209, K.253, Y.276, V.278, S.279, Y.318 9 PLIP interactions: 9 interactions with chain H Hydrophobic interactions: H:F.84, H:Y.206, H:F.209, H:F.209, H:K.253, H:Y.276, H:Y.276 Hydrogen bonds: H:S.279 Salt bridges: H:K.253

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: E.238 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.238, H2O.4, H2O.4, H2O.4, H2O.5 MG.4: 1 residues within 4Å: Chain B: E.238 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.238, H2O.11, H2O.11, H2O.12, H2O.12 MG.6: 1 residues within 4Å: Chain C: E.238 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.238, H2O.16, H2O.16, H2O.16, H2O.18 MG.8: 1 residues within 4Å: Chain D: E.238 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.238, H2O.23, H2O.23, H2O.24, H2O.24 MG.10: 1 residues within 4Å: Chain E: E.238 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:E.238, H2O.29, H2O.29, H2O.29, H2O.30 MG.12: 1 residues within 4Å: Chain F: E.238 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:E.238, H2O.36, H2O.36, H2O.37, H2O.37 MG.14: 1 residues within 4Å: Chain G: E.238 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:E.238, H2O.41, H2O.41, H2O.41, H2O.43 MG.16: 1 residues within 4Å: Chain H: E.238 5 PLIP interactions: 1 interactions with chain H, 4 Ligand-Water interactions Metal complexes: H:E.238, H2O.48, H2O.48, H2O.49, H2O.49

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Coates, L. et al., The X-ray structure of the plant like 5-aminolaevulinic acid dehydratase from Chlorobium vibrioforme complexed with the inhibitor laevulinic acid at 2.6 A resolution. J. Mol. Biol. (2004)

Release Date

2004-09-02

Peptides

DELTA-AMINOLEVULINIC ACID DEHYDRATASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

DELTA-AMINOLEVULINIC ACID DEHYDRATASE

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