SMTL ID : 1l6s.1

Crystal Structure of Porphobilinogen Synthase Complexed with the Inhibitor 4,7-Dioxosebacic Acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 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.142 ZN.3: 3 residues within 4Å: Chain B: C.119, C.121, C.129 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.119, B:C.121, B:C.129, H2O.401 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.639 ZN.9: 3 residues within 4Å: Chain D: C.119, C.121, C.129 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.119, D:C.121, D:C.129, H2O.898 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.1136 ZN.15: 3 residues within 4Å: Chain F: C.119, C.121, C.129 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:C.119, F:C.121, F:C.129, H2O.1395 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.1633 ZN.21: 3 residues within 4Å: Chain H: C.119, C.121, C.129 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:C.119, H:C.121, H:C.129, H2O.1892

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.2, H2O.12, H2O.16, H2O.19, H2O.42 MG.4: 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.264, H2O.268, H2O.271, H2O.273, H2O.284 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.499, H2O.509, H2O.513, H2O.516, H2O.539 MG.10: 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.761, H2O.765, H2O.768, H2O.770, H2O.781 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.996, H2O.1006, H2O.1010, H2O.1013, H2O.1036 MG.16: 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.1258, H2O.1262, H2O.1265, H2O.1267, H2O.1278 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.1493, H2O.1503, H2O.1507, H2O.1510, H2O.1533 MG.22: 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.1755, H2O.1759, H2O.1762, H2O.1764, H2O.1775

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

DSB.5: 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 20 PLIP interactions: 20 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:Y.269, A:Y.269, A:S.272, A:Y.311 Water bridges: A:R.215 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 16 PLIP interactions: 16 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:K.246, B:Y.269 Hydrogen bonds: 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.11: 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 20 PLIP interactions: 20 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:Y.269, C:Y.269, C:S.272, C:Y.311 Water bridges: C:R.215 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 16 PLIP interactions: 16 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:K.246, D:Y.269 Hydrogen bonds: 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.17: 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 20 PLIP interactions: 20 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:Y.269, E:Y.269, E:S.272, E:Y.311 Water bridges: E:R.215 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 16 PLIP interactions: 16 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:K.246, F:Y.269 Hydrogen bonds: 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.23: 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 20 PLIP interactions: 20 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:Y.269, G:Y.269, G:S.272, G:Y.311 Water bridges: G:R.215 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 16 PLIP interactions: 16 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:K.246, H:Y.269 Hydrogen bonds: 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

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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