SMTL ID : 1i8j.1

CRYSTAL STRUCTURE OF PORPHOBILINOGEN SYNTHASE COMPLEXED WITH THE INHIBITOR 4,7-DIOXOSEBACIC ACID

Coordinates

PDB Format Compare

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.4: 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.12 ZN.7: 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.18 ZN.10: 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.24 ZN.13: 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.30 ZN.16: 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.36 ZN.19: 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.43 ZN.22: 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.49

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.5: 2 residues within 4Å: Chain B: E.231, D.235 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.231, H2O.7, H2O.7, H2O.7, H2O.7, H2O.8 MG.8: 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.13, H2O.13, H2O.13, H2O.13, H2O.14 MG.11: 2 residues within 4Å: Chain D: E.231, D.235 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:E.231, H2O.19, H2O.19, H2O.19, H2O.19, H2O.20 MG.14: 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.25, H2O.25, H2O.25, H2O.26, H2O.26 MG.17: 2 residues within 4Å: Chain F: E.231, D.235 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:E.231, H2O.31, H2O.31, H2O.32, H2O.32, H2O.32 MG.20: 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.37, H2O.37, H2O.38, H2O.38, H2O.39 MG.23: 2 residues within 4Å: Chain H: E.231, D.235 6 PLIP interactions: 1 interactions with chain H, 5 Ligand-Water interactions Metal complexes: H:E.231, H2O.43, H2O.44, H2O.44, H2O.44, H2O.44

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

DSB.3: 14 residues within 4Å: Chain A: S.164, Y.191, K.194, F.199, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:K.194, A:Y.200, A:Y.200, A:F.203, A:F.203, A:F.203, A:K.246, A:Y.269, A:Y.269 Hydrogen bonds: A:Q.219, A:Q.219, A:Y.269, A:Y.269, A:S.272, A:Y.311 Water bridges: A:S.209 Salt bridges: A:K.194, A:R.204, A:R.215, A:K.246, A:K.246 DSB.6: 15 residues within 4Å: Chain B: F.78, S.164, Y.191, K.194, F.199, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.78, B:Y.191, B:K.194, B:Y.200, B:F.203, B:F.203, B:F.203, B:Y.269 Hydrogen bonds: B:Q.219, B:S.272, B:Y.311 Water bridges: B:R.215 Salt bridges: B:K.194, B:R.204, B:R.215, B:K.246, B:K.246 DSB.9: 14 residues within 4Å: Chain C: S.164, Y.191, K.194, F.199, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:K.194, C:Y.200, C:Y.200, C:F.203, C:F.203, C:F.203, C:K.246, C:Y.269, C:Y.269 Hydrogen bonds: C:Q.219, C:Q.219, C:Y.269, C:Y.269, C:S.272, C:Y.311 Water bridges: C:S.209 Salt bridges: C:K.194, C:R.204, C:R.215, C:K.246, C:K.246 DSB.12: 15 residues within 4Å: Chain D: F.78, S.164, Y.191, K.194, F.199, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:F.78, D:Y.191, D:K.194, D:Y.200, D:F.203, D:F.203, D:F.203, D:Y.269 Hydrogen bonds: D:Q.219, D:S.272, D:Y.311 Water bridges: D:R.215 Salt bridges: D:K.194, D:R.204, D:R.215, D:K.246, D:K.246 DSB.15: 14 residues within 4Å: Chain E: S.164, Y.191, K.194, F.199, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 21 PLIP interactions: 21 interactions with chain E Hydrophobic interactions: E:K.194, E:Y.200, E:Y.200, E:F.203, E:F.203, E:F.203, E:K.246, E:Y.269, E:Y.269 Hydrogen bonds: E:Q.219, E:Q.219, E:Y.269, E:Y.269, E:S.272, E:Y.311 Water bridges: E:S.209 Salt bridges: E:K.194, E:R.204, E:R.215, E:K.246, E:K.246 DSB.18: 15 residues within 4Å: Chain F: F.78, S.164, Y.191, K.194, F.199, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:F.78, F:Y.191, F:K.194, F:Y.200, F:F.203, F:F.203, F:F.203, F:Y.269 Hydrogen bonds: F:Q.219, F:S.272, F:Y.311 Water bridges: F:R.215 Salt bridges: F:K.194, F:R.204, F:R.215, F:K.246, F:K.246 DSB.21: 14 residues within 4Å: Chain G: S.164, Y.191, K.194, F.199, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 21 PLIP interactions: 21 interactions with chain G Hydrophobic interactions: G:K.194, G:Y.200, G:Y.200, G:F.203, G:F.203, G:F.203, G:K.246, G:Y.269, G:Y.269 Hydrogen bonds: G:Q.219, G:Q.219, G:Y.269, G:Y.269, G:S.272, G:Y.311 Water bridges: G:S.209 Salt bridges: G:K.194, G:R.204, G:R.215, G:K.246, G:K.246 DSB.24: 15 residues within 4Å: Chain H: F.78, S.164, Y.191, K.194, F.199, Y.200, F.203, R.204, R.215, Q.219, K.246, Y.269, V.271, S.272, Y.311 17 PLIP interactions: 17 interactions with chain H Hydrophobic interactions: H:F.78, H:Y.191, H:K.194, H:Y.200, H:F.203, H:F.203, H:F.203, H:Y.269 Hydrogen bonds: H:Q.219, H:S.272, H:Y.311 Water bridges: H:R.215 Salt bridges: H:K.194, H:R.204, H:R.215, H:K.246, H:K.246

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kervinen, J. et al., Mechanistic basis for suicide inactivation of porphobilinogen synthase by 4,7-dioxosebacic acid, an inhibitor that shows dramatic species selectivity. Biochemistry (2001)

Release Date

2001-06-20

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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