SMTL ID : 2c1h.1

The X-ray Structure of Chlorobium vibrioforme 5-Aminolaevulinic Acid Dehydratase Complexed with a Diacid Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: M.173, R.176, E.238, D.242 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.238, H2O.3, H2O.3, H2O.3, H2O.4 MG.3: 3 residues within 4Å: Chain B: R.176, E.238, D.242 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.238, H2O.8, H2O.8, H2O.9, H2O.9 MG.5: 4 residues within 4Å: Chain C: M.173, R.176, E.238, D.242 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.238, H2O.13, H2O.13, H2O.13, H2O.14 MG.7: 3 residues within 4Å: Chain D: R.176, E.238, D.242 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.238, H2O.18, H2O.18, H2O.19, H2O.19 MG.9: 4 residues within 4Å: Chain E: M.173, R.176, E.238, D.242 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:E.238, H2O.23, H2O.23, H2O.23, H2O.24 MG.11: 3 residues within 4Å: Chain F: R.176, E.238, D.242 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:E.238, H2O.28, H2O.28, H2O.28, H2O.29 MG.13: 4 residues within 4Å: Chain G: M.173, R.176, E.238, D.242 5 PLIP interactions: 1 interactions with chain G, 4 Ligand-Water interactions Metal complexes: G:E.238, H2O.32, H2O.33, H2O.33, H2O.33 MG.15: 3 residues within 4Å: Chain H: R.176, E.238, D.242 5 PLIP interactions: 1 interactions with chain H, 4 Ligand-Water interactions Metal complexes: H:E.238, H2O.37, H2O.37, H2O.38, H2O.38

8 x DSB: 4,7-DIOXOSEBACIC ACID(Covalent)

DSB.2: 12 residues within 4Å: Chain A: S.170, K.200, F.205, Y.206, F.209, R.210, K.222, K.253, Y.276, V.278, S.279, Y.318 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.200, A:Y.206, A:Y.206, A:F.209, A:F.209, A:F.209, A:K.253, A:Y.276 Hydrogen bonds: A:S.279, A:Y.318, A:Y.318 Salt bridges: A:K.200, A:R.210, A:K.222, A:K.253 DSB.4: 12 residues within 4Å: Chain B: D.127, S.170, K.200, Y.206, F.209, R.210, K.222, K.253, Y.276, V.278, S.279, Y.318 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:K.200, B:Y.206, B:F.209, B:F.209, B:F.209, B:K.253, B:Y.276, B:V.278 Hydrogen bonds: B:S.279, B:Y.318 Water bridges: B:D.127, B:F.209, B:R.210, B:R.210, B:R.210 Salt bridges: B:K.200, B:R.210, B:K.222, B:K.253 DSB.6: 12 residues within 4Å: Chain C: S.170, K.200, F.205, Y.206, F.209, R.210, K.222, K.253, Y.276, V.278, S.279, Y.318 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:K.200, C:Y.206, C:Y.206, C:F.209, C:F.209, C:F.209, C:K.253, C:Y.276 Hydrogen bonds: C:S.279, C:Y.318, C:Y.318 Salt bridges: C:K.200, C:R.210, C:K.222, C:K.253 DSB.8: 12 residues within 4Å: Chain D: D.127, S.170, K.200, Y.206, F.209, R.210, K.222, K.253, Y.276, V.278, S.279, Y.318 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:K.200, D:Y.206, D:F.209, D:F.209, D:F.209, D:K.253, D:Y.276, D:V.278 Hydrogen bonds: D:S.279, D:Y.318 Water bridges: D:D.127, D:F.209, D:R.210, D:R.210, D:R.210 Salt bridges: D:K.200, D:R.210, D:K.222, D:K.253 DSB.10: 12 residues within 4Å: Chain E: S.170, K.200, F.205, Y.206, F.209, R.210, K.222, K.253, Y.276, V.278, S.279, Y.318 15 PLIP interactions: 15 interactions with chain E Hydrophobic interactions: E:K.200, E:Y.206, E:Y.206, E:F.209, E:F.209, E:F.209, E:K.253, E:Y.276 Hydrogen bonds: E:S.279, E:Y.318, E:Y.318 Salt bridges: E:K.200, E:R.210, E:K.222, E:K.253 DSB.12: 12 residues within 4Å: Chain F: D.127, S.170, K.200, Y.206, F.209, R.210, K.222, K.253, Y.276, V.278, S.279, Y.318 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:K.200, F:Y.206, F:F.209, F:F.209, F:F.209, F:K.253, F:Y.276, F:V.278 Hydrogen bonds: F:S.279, F:Y.318 Water bridges: F:D.127, F:F.209, F:R.210, F:R.210, F:R.210 Salt bridges: F:K.200, F:R.210, F:K.222, F:K.253 DSB.14: 12 residues within 4Å: Chain G: S.170, K.200, F.205, Y.206, F.209, R.210, K.222, K.253, Y.276, V.278, S.279, Y.318 15 PLIP interactions: 15 interactions with chain G Hydrophobic interactions: G:K.200, G:Y.206, G:Y.206, G:F.209, G:F.209, G:F.209, G:K.253, G:Y.276 Hydrogen bonds: G:S.279, G:Y.318, G:Y.318 Salt bridges: G:K.200, G:R.210, G:K.222, G:K.253 DSB.16: 12 residues within 4Å: Chain H: D.127, S.170, K.200, Y.206, F.209, R.210, K.222, K.253, Y.276, V.278, S.279, Y.318 19 PLIP interactions: 19 interactions with chain H Hydrophobic interactions: H:K.200, H:Y.206, H:F.209, H:F.209, H:F.209, H:K.253, H:Y.276, H:V.278 Hydrogen bonds: H:S.279, H:Y.318 Water bridges: H:D.127, H:F.209, H:R.210, H:R.210, H:R.210 Salt bridges: H:K.200, H:R.210, H:K.222, H:K.253

Links

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Citation

Coates, L. et al., Structure of Chlorobium Vibrioforme 5-Aminolaevulinic Acid Dehydratase Complexed with a Diacid Inhibitor. Acta Crystallogr.,Sect.D (2005)

Release Date

2005-12-02

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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