SMTL ID : 5mhb.1

Product-Complex of E.coli 5-Amino Laevulinic Acid Dehydratase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-octamer

Ligands

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

PBG.1: 17 residues within 4Å: Chain A: F.79, D.118, C.120, C.122, S.165, K.195, Y.201, F.204, R.205, R.216, Q.220, K.247, Y.270, V.272, S.273, Y.312 Ligands: ZN.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:Y.201, A:F.204, A:F.204, A:F.204, A:Y.270 Hydrogen bonds: A:D.118, A:S.165, A:S.165, A:K.195, A:Q.220, A:K.247, A:S.273, A:Y.312 Salt bridges: A:K.195, A:R.205, A:R.216 pi-Stacking: A:F.204 pi-Cation interactions: A:K.195 PBG.8: 17 residues within 4Å: Chain B: F.79, D.118, C.120, C.122, S.165, K.195, Y.201, F.204, R.205, R.216, Q.220, K.247, Y.270, V.272, S.273, Y.312 Ligands: ZN.10 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:Y.201, B:F.204, B:F.204, B:F.204, B:Y.270 Hydrogen bonds: B:D.118, B:S.165, B:S.165, B:K.195, B:Q.220, B:K.247, B:S.273, B:Y.312 Salt bridges: B:K.195, B:R.205, B:R.216 pi-Stacking: B:F.204 pi-Cation interactions: B:K.195 PBG.15: 17 residues within 4Å: Chain C: F.79, D.118, C.120, C.122, S.165, K.195, Y.201, F.204, R.205, R.216, Q.220, K.247, Y.270, V.272, S.273, Y.312 Ligands: ZN.17 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:Y.201, C:F.204, C:F.204, C:F.204, C:Y.270 Hydrogen bonds: C:D.118, C:S.165, C:S.165, C:K.195, C:Q.220, C:K.247, C:S.273, C:Y.312 Salt bridges: C:K.195, C:R.205, C:R.216 pi-Stacking: C:F.204 pi-Cation interactions: C:K.195 PBG.22: 17 residues within 4Å: Chain D: F.79, D.118, C.120, C.122, S.165, K.195, Y.201, F.204, R.205, R.216, Q.220, K.247, Y.270, V.272, S.273, Y.312 Ligands: ZN.24 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:Y.201, D:F.204, D:F.204, D:F.204, D:Y.270 Hydrogen bonds: D:D.118, D:S.165, D:S.165, D:K.195, D:Q.220, D:K.247, D:S.273, D:Y.312 Salt bridges: D:K.195, D:R.205, D:R.216 pi-Stacking: D:F.204 pi-Cation interactions: D:K.195 PBG.29: 17 residues within 4Å: Chain E: F.79, D.118, C.120, C.122, S.165, K.195, Y.201, F.204, R.205, R.216, Q.220, K.247, Y.270, V.272, S.273, Y.312 Ligands: ZN.31 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:Y.201, E:F.204, E:F.204, E:F.204, E:Y.270 Hydrogen bonds: E:D.118, E:S.165, E:S.165, E:K.195, E:Q.220, E:K.247, E:S.273 Salt bridges: E:K.195, E:R.205, E:R.216 pi-Stacking: E:F.204 pi-Cation interactions: E:K.195 PBG.36: 17 residues within 4Å: Chain F: F.79, D.118, C.120, C.122, S.165, K.195, Y.201, F.204, R.205, R.216, Q.220, K.247, Y.270, V.272, S.273, Y.312 Ligands: ZN.38 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:Y.201, F:F.204, F:F.204, F:F.204, F:Y.270 Hydrogen bonds: F:D.118, F:S.165, F:S.165, F:K.195, F:Q.220, F:K.247, F:S.273 Salt bridges: F:K.195, F:R.205, F:R.216 pi-Stacking: F:F.204 pi-Cation interactions: F:K.195 PBG.43: 17 residues within 4Å: Chain G: F.79, D.118, C.120, C.122, S.165, K.195, Y.201, F.204, R.205, R.216, Q.220, K.247, Y.270, V.272, S.273, Y.312 Ligands: ZN.45 17 PLIP interactions: 17 interactions with chain G Hydrophobic interactions: G:Y.201, G:F.204, G:F.204, G:F.204, G:Y.270 Hydrogen bonds: G:D.118, G:S.165, G:S.165, G:K.195, G:Q.220, G:K.247, G:S.273 Salt bridges: G:K.195, G:R.205, G:R.216 pi-Stacking: G:F.204 pi-Cation interactions: G:K.195 PBG.50: 17 residues within 4Å: Chain H: F.79, D.118, C.120, C.122, S.165, K.195, Y.201, F.204, R.205, R.216, Q.220, K.247, Y.270, V.272, S.273, Y.312 Ligands: ZN.52 18 PLIP interactions: 18 interactions with chain H Hydrophobic interactions: H:Y.201, H:F.204, H:F.204, H:F.204, H:Y.270 Hydrogen bonds: H:D.118, H:S.165, H:K.195, H:Q.220, H:K.247, H:S.273 Water bridges: H:S.165, H:A.166 Salt bridges: H:K.195, H:R.205, H:R.216 pi-Stacking: H:F.204 pi-Cation interactions: H:K.195

24 x ZN: ZINC ION(Non-covalent)

ZN.2: 2 residues within 4Å: Chain A: E.40, H.84 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.40, A:E.40, A:H.84 ZN.3: 4 residues within 4Å: Chain A: C.120, C.122, C.130 Ligands: PBG.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.120, A:C.122, A:C.130 ZN.4: 2 residues within 4Å: Chain A: E.232, D.236 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.232, H2O.1, H2O.2, H2O.3, H2O.4, H2O.10 ZN.9: 2 residues within 4Å: Chain B: E.40, H.84 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.40, B:E.40, B:H.84 ZN.10: 4 residues within 4Å: Chain B: C.120, C.122, C.130 Ligands: PBG.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.120, B:C.122, B:C.130 ZN.11: 2 residues within 4Å: Chain B: E.232, D.236 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.232, H2O.14, H2O.14, H2O.15, H2O.16, H2O.22 ZN.16: 2 residues within 4Å: Chain C: E.40, H.84 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.40, C:E.40, C:H.84 ZN.17: 4 residues within 4Å: Chain C: C.120, C.122, C.130 Ligands: PBG.15 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.120, C:C.122, C:C.130 ZN.18: 2 residues within 4Å: Chain C: E.232, D.236 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.232, H2O.26, H2O.27, H2O.28, H2O.29, H2O.35 ZN.23: 2 residues within 4Å: Chain D: E.40, H.84 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.40, D:E.40, D:H.84 ZN.24: 4 residues within 4Å: Chain D: C.120, C.122, C.130 Ligands: PBG.22 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.120, D:C.122, D:C.130 ZN.25: 2 residues within 4Å: Chain D: E.232, D.236 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:E.232, H2O.39, H2O.40, H2O.41, H2O.41, H2O.47 ZN.30: 2 residues within 4Å: Chain E: E.40, H.84 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.40, E:E.40, E:H.84 ZN.31: 4 residues within 4Å: Chain E: C.120, C.122, C.130 Ligands: PBG.29 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.120, E:C.122, E:C.130 ZN.32: 2 residues within 4Å: Chain E: E.232, D.236 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:E.232, H2O.51, H2O.52, H2O.53, H2O.54, H2O.60 ZN.37: 2 residues within 4Å: Chain F: E.40, H.84 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.40, F:E.40, F:H.84 ZN.38: 4 residues within 4Å: Chain F: C.120, C.122, C.130 Ligands: PBG.36 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.120, F:C.122, F:C.130 ZN.39: 2 residues within 4Å: Chain F: E.232, D.236 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:E.232, H2O.64, H2O.65, H2O.66, H2O.67, H2O.73 ZN.44: 2 residues within 4Å: Chain G: E.40, H.84 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.40, G:E.40, G:H.84 ZN.45: 4 residues within 4Å: Chain G: C.120, C.122, C.130 Ligands: PBG.43 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.120, G:C.122, G:C.130 ZN.46: 2 residues within 4Å: Chain G: E.232, D.236 6 PLIP interactions: 1 interactions with chain G, 5 Ligand-Water interactions Metal complexes: G:E.232, H2O.77, H2O.77, H2O.78, H2O.79, H2O.85 ZN.51: 2 residues within 4Å: Chain H: E.40, H.84 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.40, H:E.40, H:H.84 ZN.52: 4 residues within 4Å: Chain H: C.120, C.122, C.130 Ligands: PBG.50 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:C.120, H:C.122, H:C.130 ZN.53: 2 residues within 4Å: Chain H: E.232, D.236 6 PLIP interactions: 1 interactions with chain H, 5 Ligand-Water interactions Metal complexes: H:E.232, H2O.89, H2O.90, H2O.91, H2O.92, H2O.98

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: L.26, L.295, E.296 Chain G: M.224 Ligand excluded by PLIP GOL.6: 7 residues within 4Å: Chain A: E.290, E.291, F.313, D.316, L.317, K.320, I.322 Ligand excluded by PLIP GOL.7: 6 residues within 4Å: Chain A: A.197, S.199, D.215, R.216, K.217 Chain G: K.292 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain B: L.26, L.295, E.296 Chain H: M.224 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain B: E.290, E.291, F.313, D.316, L.317, K.320, I.322 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain B: A.197, S.199, D.215, R.216, K.217 Chain H: K.292 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain C: L.26, L.295, E.296 Chain E: M.224 Ligand excluded by PLIP GOL.20: 7 residues within 4Å: Chain C: E.290, E.291, F.313, D.316, L.317, K.320, I.322 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain C: A.197, S.199, D.215, R.216, K.217 Chain E: K.292 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain D: L.26, L.295, E.296 Chain F: M.224 Ligand excluded by PLIP GOL.27: 7 residues within 4Å: Chain D: E.290, E.291, F.313, D.316, L.317, K.320, I.322 Ligand excluded by PLIP GOL.28: 6 residues within 4Å: Chain D: A.197, S.199, D.215, R.216, K.217 Chain F: K.292 Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain C: M.224 Chain E: L.26, L.295, E.296 Ligand excluded by PLIP GOL.34: 7 residues within 4Å: Chain E: E.290, E.291, F.313, D.316, L.317, K.320, I.322 Ligand excluded by PLIP GOL.35: 6 residues within 4Å: Chain C: K.292 Chain E: A.197, S.199, D.215, R.216, K.217 Ligand excluded by PLIP GOL.40: 4 residues within 4Å: Chain D: M.224 Chain F: L.26, L.295, E.296 Ligand excluded by PLIP GOL.41: 7 residues within 4Å: Chain F: E.290, E.291, F.313, D.316, L.317, K.320, I.322 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain D: K.292 Chain F: A.197, S.199, D.215, R.216, K.217 Ligand excluded by PLIP GOL.47: 4 residues within 4Å: Chain A: M.224 Chain G: L.26, L.295, E.296 Ligand excluded by PLIP GOL.48: 7 residues within 4Å: Chain G: E.290, E.291, F.313, D.316, L.317, K.320, I.322 Ligand excluded by PLIP GOL.49: 6 residues within 4Å: Chain A: K.292 Chain G: A.197, S.199, D.215, R.216, K.217 Ligand excluded by PLIP GOL.54: 4 residues within 4Å: Chain B: M.224 Chain H: L.26, L.295, E.296 Ligand excluded by PLIP GOL.55: 7 residues within 4Å: Chain H: E.290, E.291, F.313, D.316, L.317, K.320, I.322 Ligand excluded by PLIP GOL.56: 6 residues within 4Å: Chain B: K.292 Chain H: A.197, S.199, D.215, R.216, K.217 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mills-Davies, N. et al., Structural studies of substrate and product complexes of 5-aminolaevulinic acid dehydratase from humans, Escherichia coli and the hyperthermophile Pyrobaculum calidifontis. Acta Crystallogr D Struct Biol (2017)

Release Date

2016-12-07

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