SMTL ID : 1l6y.1

Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4-Oxosebacic Acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-octamer

Ligands

8 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.119, C.121, C.129, S.164 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.119, A:C.121, A:C.129, H2O.6 ZN.8: 4 residues within 4Å: Chain B: C.119, C.121, C.129, S.164 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.119, B:C.121, B:C.129, H2O.14 ZN.12: 4 residues within 4Å: Chain C: C.119, C.121, C.129, S.164 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.119, C:C.121, C:C.129, H2O.22 ZN.19: 4 residues within 4Å: Chain D: C.119, C.121, C.129, S.164 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.119, D:C.121, D:C.129, H2O.31 ZN.23: 4 residues within 4Å: Chain E: C.119, C.121, C.129, S.164 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:C.119, E:C.121, E:C.129, H2O.39 ZN.30: 4 residues within 4Å: Chain F: C.119, C.121, C.129, S.164 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:C.119, F:C.121, F:C.129, H2O.48 ZN.34: 4 residues within 4Å: Chain G: C.119, C.121, C.129, S.164 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:C.119, G:C.121, G:C.129, H2O.55 ZN.41: 4 residues within 4Å: Chain H: C.119, C.121, C.129, S.164 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:C.119, H:C.121, H:C.129, H2O.64

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: E.231, D.235 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.231, H2O.1, H2O.1, H2O.1, H2O.1, H2O.2 MG.9: 3 residues within 4Å: Chain B: S.192, E.231, D.235 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.231, H2O.9, H2O.9, H2O.9, H2O.9, H2O.10 MG.13: 2 residues within 4Å: Chain C: E.231, D.235 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.231, H2O.17, H2O.18, H2O.18, H2O.18, H2O.19 MG.20: 3 residues within 4Å: Chain D: S.192, E.231, D.235 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:E.231, H2O.26, H2O.26, H2O.26, H2O.26, H2O.26 MG.24: 2 residues within 4Å: Chain E: E.231, D.235 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:E.231, H2O.34, H2O.34, H2O.34, H2O.34, H2O.35 MG.31: 3 residues within 4Å: Chain F: S.192, E.231, D.235 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:E.231, H2O.42, H2O.42, H2O.42, H2O.42, H2O.43 MG.35: 2 residues within 4Å: Chain G: E.231, D.235 6 PLIP interactions: 1 interactions with chain G, 5 Ligand-Water interactions Metal complexes: G:E.231, H2O.50, H2O.51, H2O.51, H2O.51, H2O.52 MG.42: 3 residues within 4Å: Chain H: S.192, E.231, D.235 6 PLIP interactions: 1 interactions with chain H, 5 Ligand-Water interactions Metal complexes: H:E.231, H2O.59, H2O.59, H2O.59, H2O.59, H2O.59

8 x 4OX: 4-OXODECANEDIOIC ACID(Covalent)

4OX.3: 12 residues within 4Å: Chain A: S.164, K.194, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.200, A:Y.200, A:F.203, A:F.203, A:F.203, A:F.203, A:V.271 Hydrogen bonds: A:S.272, A:Y.311 Water bridges: A:S.209, A:Q.219 Salt bridges: A:R.204, A:R.215, A:K.246 4OX.10: 12 residues within 4Å: Chain B: F.78, K.194, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.78, B:F.203, B:F.203, B:F.203, B:K.246, B:Y.269 Hydrogen bonds: B:S.272 Water bridges: B:R.204, B:S.209 Salt bridges: B:R.204, B:R.215, B:K.246 4OX.14: 12 residues within 4Å: Chain C: S.164, K.194, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.200, C:Y.200, C:F.203, C:F.203, C:F.203, C:F.203, C:V.271 Hydrogen bonds: C:S.272, C:Y.311 Water bridges: C:S.209, C:Q.219 Salt bridges: C:R.204, C:R.215, C:K.246 4OX.21: 12 residues within 4Å: Chain D: F.78, K.194, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.78, D:F.203, D:F.203, D:F.203, D:K.246, D:Y.269 Hydrogen bonds: D:S.272 Water bridges: D:R.204, D:S.209 Salt bridges: D:R.204, D:R.215, D:K.246 4OX.25: 12 residues within 4Å: Chain E: S.164, K.194, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:Y.200, E:Y.200, E:F.203, E:F.203, E:F.203, E:F.203, E:V.271 Hydrogen bonds: E:S.272, E:Y.311 Water bridges: E:S.209, E:Q.219 Salt bridges: E:R.204, E:R.215, E:K.246 4OX.32: 12 residues within 4Å: Chain F: F.78, K.194, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:F.78, F:F.203, F:F.203, F:F.203, F:K.246, F:Y.269 Hydrogen bonds: F:S.272 Water bridges: F:R.204, F:S.209 Salt bridges: F:R.204, F:R.215, F:K.246 4OX.36: 12 residues within 4Å: Chain G: S.164, K.194, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 14 PLIP interactions: 14 interactions with chain G Hydrophobic interactions: G:Y.200, G:Y.200, G:F.203, G:F.203, G:F.203, G:F.203, G:V.271 Hydrogen bonds: G:S.272, G:Y.311 Water bridges: G:S.209, G:Q.219 Salt bridges: G:R.204, G:R.215, G:K.246 4OX.43: 12 residues within 4Å: Chain H: F.78, K.194, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 12 PLIP interactions: 12 interactions with chain H Hydrophobic interactions: H:F.78, H:F.203, H:F.203, H:F.203, H:K.246, H:Y.269 Hydrogen bonds: H:S.272 Water bridges: H:R.204, H:S.209 Salt bridges: H:R.204, H:R.215, H:K.246

20 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 4 residues within 4Å: Chain A: T.87, S.89, W.92, K.148 Ligand excluded by PLIP GOL.5: 2 residues within 4Å: Chain A: E.144, K.148 Ligand excluded by PLIP GOL.6: 6 residues within 4Å: Chain A: S.13 Chain F: K.106, P.110, E.111, I.113, D.159 Ligand excluded by PLIP GOL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain B: L.27, A.70, G.71, R.323 Ligand excluded by PLIP GOL.15: 4 residues within 4Å: Chain C: T.87, S.89, W.92, K.148 Ligand excluded by PLIP GOL.16: 2 residues within 4Å: Chain C: E.144, K.148 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain C: S.13 Chain H: K.106, P.110, E.111, I.113, D.159 Ligand excluded by PLIP GOL.18: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain D: L.27, A.70, G.71, R.323 Ligand excluded by PLIP GOL.26: 4 residues within 4Å: Chain E: T.87, S.89, W.92, K.148 Ligand excluded by PLIP GOL.27: 2 residues within 4Å: Chain E: E.144, K.148 Ligand excluded by PLIP GOL.28: 6 residues within 4Å: Chain D: K.106, P.110, E.111, I.113, D.159 Chain E: S.13 Ligand excluded by PLIP GOL.29: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.33: 4 residues within 4Å: Chain F: L.27, A.70, G.71, R.323 Ligand excluded by PLIP GOL.37: 4 residues within 4Å: Chain G: T.87, S.89, W.92, K.148 Ligand excluded by PLIP GOL.38: 2 residues within 4Å: Chain G: E.144, K.148 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain B: K.106, P.110, E.111, I.113, D.159 Chain G: S.13 Ligand excluded by PLIP GOL.40: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP GOL.44: 4 residues within 4Å: Chain H: L.27, A.70, G.71, R.323 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jaffe, E.K. et al., Species-Specific Inhibition of Porphobilinogen Synthase by 4-Oxosebacic Acid. J.Biol.Chem. (2002)

Release Date

2002-04-17

Peptides

PORPHOBILINOGEN SYNTHASE: 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

PORPHOBILINOGEN SYNTHASE

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