SMTL ID : 2c16.1

5-(4-Carboxy-2-oxo-butane-1-sulfinyl)-4-oxo-pentanoic acid acid bound to Porphobilinogen synthase from Pseudomonas aeruginosa

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.02 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 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.9, H2O.10, H2O.11, H2O.11, H2O.11 MG.5: 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.22, H2O.22, H2O.24, H2O.24, H2O.24 MG.9: 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.35, H2O.35, H2O.36, H2O.36, H2O.36 MG.13: 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.47, H2O.47, H2O.49, H2O.49, H2O.49 MG.17: 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.60, H2O.60, H2O.61, H2O.62, H2O.62 MG.21: 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.72, H2O.72, H2O.74, H2O.74, H2O.74 MG.25: 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.85, H2O.85, H2O.87, H2O.87, H2O.87 MG.29: 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.97, H2O.98, H2O.99, H2O.99, H2O.99

8 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.2: 4 residues within 4Å: Chain A: D.97, V.152, V.156 Ligands: PGE.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.155, A:D.155 PGE.3: 7 residues within 4Å: Chain A: I.141, L.142, D.143, D.144, L.149, V.152 Ligands: PGE.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.144 PGE.10: 4 residues within 4Å: Chain C: D.97, V.152, V.156 Ligands: PGE.11 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.155, C:D.155 PGE.11: 7 residues within 4Å: Chain C: I.141, L.142, D.143, D.144, L.149, V.152 Ligands: PGE.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.144 PGE.18: 4 residues within 4Å: Chain E: D.97, V.152, V.156 Ligands: PGE.19 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.155, E:D.155 PGE.19: 7 residues within 4Å: Chain E: I.141, L.142, D.143, D.144, L.149, V.152 Ligands: PGE.18 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.144 PGE.26: 4 residues within 4Å: Chain G: D.97, V.152, V.156 Ligands: PGE.27 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:D.155, G:D.155 PGE.27: 7 residues within 4Å: Chain G: I.141, L.142, D.143, D.144, L.149, V.152 Ligands: PGE.26 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.144

12 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 4 residues within 4Å: Chain A: G.183, A.251, E.252 Chain D: Y.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.183 Water bridges: A:A.184 PEG.7: 4 residues within 4Å: Chain B: G.183, A.251, E.252 Chain E: Y.12 No protein-ligand interaction detected (PLIP) PEG.8: 6 residues within 4Å: Chain B: R.62, V.88, R.215, D.216, V.218, G.219 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.218 Water bridges: B:R.62 PEG.12: 4 residues within 4Å: Chain C: G.183, A.251, E.252 Chain H: Y.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.183 Water bridges: C:A.184 PEG.15: 4 residues within 4Å: Chain A: Y.12 Chain D: G.183, A.251, E.252 No protein-ligand interaction detected (PLIP) PEG.16: 6 residues within 4Å: Chain D: R.62, V.88, R.215, D.216, V.218, G.219 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.218 Water bridges: D:R.62 PEG.20: 4 residues within 4Å: Chain B: Y.12 Chain E: G.183, A.251, E.252 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.183 Water bridges: E:A.184 PEG.23: 4 residues within 4Å: Chain F: G.183, A.251, E.252 Chain G: Y.12 No protein-ligand interaction detected (PLIP) PEG.24: 6 residues within 4Å: Chain F: R.62, V.88, R.215, D.216, V.218, G.219 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:V.218 Water bridges: F:R.62 PEG.28: 4 residues within 4Å: Chain F: Y.12 Chain G: G.183, A.251, E.252 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.183 Water bridges: G:A.184 PEG.31: 4 residues within 4Å: Chain C: Y.12 Chain H: G.183, A.251, E.252 No protein-ligand interaction detected (PLIP) PEG.32: 6 residues within 4Å: Chain H: R.62, V.88, R.215, D.216, V.218, G.219 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:V.218 Water bridges: H:R.62

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 4 residues within 4Å: Chain B: H.194, T.195, N.196, V.197 Ligand excluded by PLIP CL.14: 4 residues within 4Å: Chain D: H.194, T.195, N.196, V.197 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain F: H.194, T.195, N.196, V.197 Ligand excluded by PLIP CL.30: 4 residues within 4Å: Chain H: H.194, T.195, N.196, V.197 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frere, F. et al., Probing the Active Site of Pseudomonas Aeruginosa Porphobilinogen Synthase Using Newly Developed Inhibitors. Biochemistry (2006)

Release Date

2006-06-20

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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