SMTL ID : 1gzg.1

Complex of a Mg2-dependent porphobilinogen synthase from Pseudomonas aeruginosa (mutant D139N) with 5-fluorolevulinic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.66 Å

Oligo State

homo-octamer

Ligands

16 x LAF: 5-FLUOROLEVULINIC ACID(Covalent)(Non-covalent)

LAF.1: 12 residues within 4Å: Chain A: A.129, D.131, N.139, S.175, K.205, Y.211, R.215, K.229, Q.233, K.260 Ligands: LAF.2, NA.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.205 Hydrogen bonds: A:Q.233 Water bridges: A:K.229 Salt bridges: A:K.205, A:R.215, A:K.229 LAF.2: 13 residues within 4Å: Chain A: F.86, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: LAF.1, NA.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.211, A:F.214, A:K.260, A:Y.283 Hydrogen bonds: A:Y.283, A:Y.283, A:S.286, A:Y.324 Salt bridges: A:K.260 LAF.6: 11 residues within 4Å: Chain B: A.129, D.131, N.139, S.175, K.205, Y.211, R.215, K.229, Q.233 Ligands: LAF.7, NA.11 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:K.205, B:Q.233 Water bridges: B:D.131 Salt bridges: B:K.205, B:R.215, B:K.229 Halogen bonds: B:N.139 LAF.7: 13 residues within 4Å: Chain B: F.86, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: LAF.6, NA.11 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.211, B:F.214, B:K.260, B:Y.283 Hydrogen bonds: B:Y.211, B:S.286 Salt bridges: B:K.260 LAF.13: 12 residues within 4Å: Chain C: A.129, D.131, N.139, S.175, K.205, Y.211, R.215, K.229, Q.233, K.260 Ligands: LAF.14, NA.16 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:K.205 Hydrogen bonds: C:Q.233 Water bridges: C:K.229 Salt bridges: C:K.205, C:R.215, C:K.229 LAF.14: 13 residues within 4Å: Chain C: F.86, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: LAF.13, NA.16 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.211, C:F.214, C:K.260, C:Y.283 Hydrogen bonds: C:Y.283, C:Y.283, C:S.286, C:Y.324 Salt bridges: C:K.260 LAF.18: 11 residues within 4Å: Chain D: A.129, D.131, N.139, S.175, K.205, Y.211, R.215, K.229, Q.233 Ligands: LAF.19, NA.23 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:K.205, D:Q.233 Water bridges: D:D.131 Salt bridges: D:K.205, D:R.215, D:K.229 Halogen bonds: D:N.139 LAF.19: 13 residues within 4Å: Chain D: F.86, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: LAF.18, NA.23 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:Y.211, D:F.214, D:K.260, D:Y.283 Hydrogen bonds: D:Y.211, D:S.286 Salt bridges: D:K.260 LAF.25: 12 residues within 4Å: Chain E: A.129, D.131, N.139, S.175, K.205, Y.211, R.215, K.229, Q.233, K.260 Ligands: LAF.26, NA.28 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:K.205 Hydrogen bonds: E:Q.233 Water bridges: E:K.229 Salt bridges: E:K.205, E:R.215, E:K.229 LAF.26: 13 residues within 4Å: Chain E: F.86, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: LAF.25, NA.28 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:Y.211, E:F.214, E:K.260, E:Y.283 Hydrogen bonds: E:Y.283, E:Y.283, E:S.286, E:Y.324 Salt bridges: E:K.260 LAF.30: 11 residues within 4Å: Chain F: A.129, D.131, N.139, S.175, K.205, Y.211, R.215, K.229, Q.233 Ligands: LAF.31, NA.35 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:K.205, F:Q.233 Water bridges: F:D.131 Salt bridges: F:K.205, F:R.215, F:K.229 Halogen bonds: F:N.139 LAF.31: 13 residues within 4Å: Chain F: F.86, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: LAF.30, NA.35 7 PLIP interactions: 7 interactions with chain F Hydrophobic interactions: F:Y.211, F:F.214, F:K.260, F:Y.283 Hydrogen bonds: F:Y.211, F:S.286 Salt bridges: F:K.260 LAF.37: 12 residues within 4Å: Chain G: A.129, D.131, N.139, S.175, K.205, Y.211, R.215, K.229, Q.233, K.260 Ligands: LAF.38, NA.40 6 PLIP interactions: 6 interactions with chain G Hydrophobic interactions: G:K.205 Hydrogen bonds: G:Q.233 Water bridges: G:K.229 Salt bridges: G:K.205, G:R.215, G:K.229 LAF.38: 13 residues within 4Å: Chain G: F.86, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: LAF.37, NA.40 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:Y.211, G:F.214, G:K.260, G:Y.283 Hydrogen bonds: G:Y.283, G:Y.283, G:S.286, G:Y.324 Salt bridges: G:K.260 LAF.42: 11 residues within 4Å: Chain H: A.129, D.131, N.139, S.175, K.205, Y.211, R.215, K.229, Q.233 Ligands: LAF.43, NA.47 7 PLIP interactions: 7 interactions with chain H Hydrogen bonds: H:K.205, H:Q.233 Water bridges: H:D.131 Salt bridges: H:K.205, H:R.215, H:K.229 Halogen bonds: H:N.139 LAF.43: 13 residues within 4Å: Chain H: F.86, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: LAF.42, NA.47 7 PLIP interactions: 7 interactions with chain H Hydrophobic interactions: H:Y.211, H:F.214, H:K.260, H:Y.283 Hydrogen bonds: H:Y.211, H:S.286 Salt bridges: H:K.260

8 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.245, H2O.10, H2O.10, H2O.12, H2O.12, H2O.12 MG.10: 3 residues within 4Å: Chain B: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.245, H2O.23, H2O.24, H2O.24, H2O.24, H2O.24 MG.15: 3 residues within 4Å: Chain C: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.245, H2O.36, H2O.36, H2O.38, H2O.38, H2O.38 MG.22: 3 residues within 4Å: Chain D: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:E.245, H2O.48, H2O.50, H2O.50, H2O.50, H2O.50 MG.27: 3 residues within 4Å: Chain E: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:E.245, H2O.61, H2O.61, H2O.63, H2O.64, H2O.64 MG.34: 3 residues within 4Å: Chain F: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:E.245, H2O.74, H2O.76, H2O.76, H2O.76, H2O.76 MG.39: 3 residues within 4Å: Chain G: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain G, 5 Ligand-Water interactions Metal complexes: G:E.245, H2O.87, H2O.87, H2O.89, H2O.89, H2O.89 MG.46: 3 residues within 4Å: Chain H: R.181, E.245, D.249 6 PLIP interactions: 1 interactions with chain H, 5 Ligand-Water interactions Metal complexes: H:E.245, H2O.100, H2O.101, H2O.101, H2O.102, H2O.102

8 x NA: SODIUM ION(Non-functional Binders)

NA.4: 6 residues within 4Å: Chain A: D.127, A.129, D.131, S.175 Ligands: LAF.1, LAF.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.127, A:S.175 NA.11: 4 residues within 4Å: Chain B: D.127, S.175 Ligands: LAF.6, LAF.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.127, B:S.175 NA.16: 6 residues within 4Å: Chain C: D.127, A.129, D.131, S.175 Ligands: LAF.13, LAF.14 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.127, C:S.175 NA.23: 4 residues within 4Å: Chain D: D.127, S.175 Ligands: LAF.18, LAF.19 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.127, D:S.175 NA.28: 6 residues within 4Å: Chain E: D.127, A.129, D.131, S.175 Ligands: LAF.25, LAF.26 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.175, E:S.175 NA.35: 4 residues within 4Å: Chain F: D.127, S.175 Ligands: LAF.30, LAF.31 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.175, F:S.175 NA.40: 6 residues within 4Å: Chain G: D.127, A.129, D.131, S.175 Ligands: LAF.37, LAF.38 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.175, G:S.175 NA.47: 4 residues within 4Å: Chain H: D.127, S.175 Ligands: LAF.42, LAF.43 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:D.127, H:S.175

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: F.119, P.120, E.121, L.122 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.121, A:L.122 Water bridges: A:R.118 SO4.12: 5 residues within 4Å: Chain B: V.76, F.119, P.120, E.121, L.122 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.121, B:L.122 SO4.17: 4 residues within 4Å: Chain C: F.119, P.120, E.121, L.122 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.121, C:L.122 Water bridges: C:R.118 SO4.24: 5 residues within 4Å: Chain D: V.76, F.119, P.120, E.121, L.122 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:E.121, D:L.122 SO4.29: 4 residues within 4Å: Chain E: F.119, P.120, E.121, L.122 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.121, E:L.122 Water bridges: E:R.118 SO4.36: 5 residues within 4Å: Chain F: V.76, F.119, P.120, E.121, L.122 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.121, F:L.122 SO4.41: 4 residues within 4Å: Chain G: F.119, P.120, E.121, L.122 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:E.121, G:L.122 Water bridges: G:R.118 SO4.48: 5 residues within 4Å: Chain H: V.76, F.119, P.120, E.121, L.122 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:E.121, H:L.122

8 x K: POTASSIUM ION(Non-covalent)

K.8: 5 residues within 4Å: Chain B: D.36, D.37, D.319 Chain E: R.26, L.27 5 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: E:L.27, B:D.37, B:D.319, H2O.54, H2O.54 K.9: 6 residues within 4Å: Chain B: R.26, L.27, R.29 Chain E: D.36, D.37, D.319 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: B:L.27, E:D.37, E:D.319, H2O.17, H2O.17 K.20: 5 residues within 4Å: Chain A: R.26, L.27 Chain D: D.36, D.37, D.319 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: A:L.27, D:D.37, D:D.319, H2O.2, H2O.2 K.21: 6 residues within 4Å: Chain A: D.36, D.37, D.319 Chain D: R.26, L.27, R.29 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: A:D.37, A:D.319, D:L.27, H2O.42, H2O.42 K.32: 5 residues within 4Å: Chain F: D.36, D.37, D.319 Chain G: R.26, L.27 5 PLIP interactions: 2 interactions with chain F, 1 interactions with chain G, 2 Ligand-Water interactions Metal complexes: F:D.37, F:D.319, G:L.27, H2O.80, H2O.80 K.33: 6 residues within 4Å: Chain F: R.26, L.27, R.29 Chain G: D.36, D.37, D.319 5 PLIP interactions: 1 interactions with chain F, 2 interactions with chain G, 2 Ligand-Water interactions Metal complexes: F:L.27, G:D.37, G:D.319, H2O.68, H2O.68 K.44: 5 residues within 4Å: Chain C: R.26, L.27 Chain H: D.36, D.37, D.319 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: C:L.27, H:D.37, H:D.319, H2O.28, H2O.28 K.45: 6 residues within 4Å: Chain C: D.36, D.37, D.319 Chain H: R.26, L.27, R.29 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain H, 2 Ligand-Water interactions Metal complexes: C:D.37, C:D.319, H:L.27, H2O.94, H2O.94

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frere, F. et al., Structure of porphobilinogen synthase from Pseudomonas aeruginosa in complex with 5-fluorolevulinic acid suggests a double Schiff base mechanism. J. Mol. Biol. (2002)

Release Date

2002-06-27

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