SMTL ID : 2woq.1

Porphobilinogen Synthase (HemB) in Complex with 5-acetamido-4- oxohexanoic acid (Alaremycin 2)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-octamer

Ligands

8 x AYC: ALAREMYCIN 2(Covalent)

AYC.1: 14 residues within 4Å: Chain A: F.86, D.127, D.131, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: MG.4 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.86, A:Y.202, A:Y.211, A:F.214, A:F.214, A:K.260, A:Y.283 Hydrogen bonds: A:K.205, A:Y.211, A:Y.283, A:S.286, A:Y.324 Water bridges: A:S.175, A:S.175, A:Q.233 Salt bridges: A:K.260 AYC.12: 14 residues within 4Å: Chain B: F.86, D.127, D.131, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: MG.15 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:F.86, B:Y.202, B:Y.211, B:F.214, B:F.214, B:K.260, B:Y.283 Hydrogen bonds: B:K.205, B:Y.211, B:S.286 Water bridges: B:S.175, B:S.175, B:Q.233 Salt bridges: B:K.260 AYC.23: 14 residues within 4Å: Chain C: F.86, D.127, D.131, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: MG.26 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:F.86, C:Y.202, C:Y.211, C:F.214, C:F.214, C:K.260, C:Y.283 Hydrogen bonds: C:K.205, C:Y.211, C:Y.283, C:S.286, C:Y.324 Water bridges: C:S.175, C:S.175, C:Q.233 Salt bridges: C:K.260 AYC.34: 14 residues within 4Å: Chain D: F.86, D.127, D.131, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: MG.37 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:F.86, D:Y.202, D:Y.211, D:F.214, D:F.214, D:K.260, D:Y.283 Hydrogen bonds: D:K.205, D:Y.211, D:S.286 Water bridges: D:S.175, D:S.175, D:Q.233 Salt bridges: D:K.260 AYC.45: 14 residues within 4Å: Chain E: F.86, D.127, D.131, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: MG.48 16 PLIP interactions: 16 interactions with chain E Hydrophobic interactions: E:F.86, E:Y.202, E:Y.211, E:F.214, E:F.214, E:K.260, E:Y.283 Hydrogen bonds: E:K.205, E:Y.211, E:Y.283, E:S.286, E:Y.324 Water bridges: E:S.175, E:S.175, E:Q.233 Salt bridges: E:K.260 AYC.56: 14 residues within 4Å: Chain F: F.86, D.127, D.131, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: MG.59 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:F.86, F:Y.202, F:Y.211, F:F.214, F:F.214, F:K.260, F:Y.283 Hydrogen bonds: F:K.205, F:Y.211, F:Y.283, F:S.286, F:Y.324 Water bridges: F:S.175, F:S.175, F:Q.233 Salt bridges: F:K.260 AYC.67: 14 residues within 4Å: Chain G: F.86, D.127, D.131, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: MG.70 14 PLIP interactions: 14 interactions with chain G Hydrophobic interactions: G:F.86, G:Y.202, G:Y.211, G:F.214, G:F.214, G:K.260, G:Y.283 Hydrogen bonds: G:K.205, G:Y.211, G:S.286 Water bridges: G:S.175, G:S.175, G:Q.233 Salt bridges: G:K.260 AYC.78: 14 residues within 4Å: Chain H: F.86, D.127, D.131, S.175, Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: MG.81 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:F.86, H:Y.202, H:Y.211, H:F.214, H:F.214, H:K.260, H:Y.283 Hydrogen bonds: H:K.205, H:Y.211, H:S.286 Water bridges: H:S.175, H:S.175, H:Q.233 Salt bridges: H:K.260

32 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.2: 1 residues within 4Å: Ligands: EPE.17 No protein-ligand interaction detected (PLIP) 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.5, H2O.5, H2O.6, H2O.6, H2O.6 MG.4: 6 residues within 4Å: Chain A: A.129, D.131, D.139, S.175, D.176 Ligands: AYC.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.131, A:D.139, A:D.176, H2O.4, H2O.5 MG.5: 4 residues within 4Å: Chain A: D.37, D.319 Chain B: L.27, R.29 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.37, A:D.319, H2O.2, H2O.8, H2O.8 MG.13: 1 residues within 4Å: Ligands: EPE.6 No protein-ligand interaction detected (PLIP) MG.14: 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.11, H2O.11, H2O.13, H2O.13, H2O.13 MG.15: 6 residues within 4Å: Chain B: A.129, D.131, D.139, S.175, D.176 Ligands: AYC.12 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.131, B:D.139, B:D.176, H2O.11, H2O.11 MG.16: 4 residues within 4Å: Chain A: L.27, R.29 Chain B: D.37, D.319 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.37, B:D.319, H2O.1, H2O.1, H2O.8 MG.24: 1 residues within 4Å: Ligands: EPE.39 No protein-ligand interaction detected (PLIP) MG.25: 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.18, H2O.18, H2O.19, H2O.19, H2O.19 MG.26: 6 residues within 4Å: Chain C: A.129, D.131, D.139, S.175, D.176 Ligands: AYC.23 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.131, C:D.139, C:D.176, H2O.17, H2O.18 MG.27: 4 residues within 4Å: Chain C: D.37, D.319 Chain D: L.27, R.29 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.37, C:D.319, H2O.15, H2O.21, H2O.22 MG.35: 1 residues within 4Å: Ligands: EPE.28 No protein-ligand interaction detected (PLIP) MG.36: 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.25, H2O.25, H2O.26, H2O.26, H2O.26 MG.37: 6 residues within 4Å: Chain D: A.129, D.131, D.139, S.175, D.176 Ligands: AYC.34 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.131, D:D.139, D:D.176, H2O.24, H2O.25 MG.38: 4 residues within 4Å: Chain C: L.27, R.29 Chain D: D.37, D.319 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.37, D:D.319, H2O.15, H2O.15, H2O.22 MG.46: 1 residues within 4Å: Ligands: EPE.72 No protein-ligand interaction detected (PLIP) MG.47: 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.32, H2O.32, H2O.33, H2O.33, H2O.33 MG.48: 6 residues within 4Å: Chain E: A.129, D.131, D.139, S.175, D.176 Ligands: AYC.45 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.131, E:D.139, E:D.176, H2O.31, H2O.32 MG.49: 4 residues within 4Å: Chain E: D.37, D.319 Chain G: L.27, R.29 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.37, E:D.319, H2O.29, H2O.42, H2O.42 MG.57: 1 residues within 4Å: Ligands: EPE.83 No protein-ligand interaction detected (PLIP) MG.58: 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.38, H2O.38, H2O.40, H2O.40, H2O.40 MG.59: 6 residues within 4Å: Chain F: A.129, D.131, D.139, S.175, D.176 Ligands: AYC.56 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.131, F:D.139, F:D.176, H2O.38, H2O.38 MG.60: 4 residues within 4Å: Chain F: D.37, D.319 Chain H: L.27, R.29 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.37, F:D.319, H2O.36, H2O.49, H2O.49 MG.68: 1 residues within 4Å: Ligands: EPE.50 No protein-ligand interaction detected (PLIP) MG.69: 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.45, H2O.45, H2O.46, H2O.46, H2O.46 MG.70: 6 residues within 4Å: Chain G: A.129, D.131, D.139, S.175, D.176 Ligands: AYC.67 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.131, G:D.139, G:D.176, H2O.45, H2O.45 MG.71: 4 residues within 4Å: Chain E: L.27, R.29 Chain G: D.37, D.319 5 PLIP interactions: 2 interactions with chain G, 3 Ligand-Water interactions Metal complexes: G:D.37, G:D.319, H2O.28, H2O.28, H2O.42 MG.79: 1 residues within 4Å: Ligands: EPE.61 No protein-ligand interaction detected (PLIP) MG.80: 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.52, H2O.52, H2O.53, H2O.53, H2O.53 MG.81: 6 residues within 4Å: Chain H: A.129, D.131, D.139, S.175, D.176 Ligands: AYC.78 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.131, H:D.139, H:D.176, H2O.51, H2O.52 MG.82: 4 residues within 4Å: Chain F: L.27, R.29 Chain H: D.37, D.319 5 PLIP interactions: 2 interactions with chain H, 3 Ligand-Water interactions Metal complexes: H:D.37, H:D.319, H2O.35, H2O.35, H2O.49

16 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.6: 10 residues within 4Å: Chain A: E.30, N.31, V.32, K.314 Chain B: E.30, N.31, V.32, K.314 Ligands: MG.13, EPE.17 Ligand excluded by PLIP EPE.7: 7 residues within 4Å: Chain A: G.193, T.195, N.196 Chain B: R.20 Chain E: D.143, Y.147, L.149 Ligand excluded by PLIP EPE.17: 10 residues within 4Å: Chain A: E.30, N.31, V.32, K.314 Chain B: E.30, N.31, V.32, K.314 Ligands: MG.2, EPE.6 Ligand excluded by PLIP EPE.18: 7 residues within 4Å: Chain A: R.20 Chain B: G.193, T.195, N.196 Chain H: D.143, Y.147, L.149 Ligand excluded by PLIP EPE.28: 10 residues within 4Å: Chain C: E.30, N.31, V.32, K.314 Chain D: E.30, N.31, V.32, K.314 Ligands: MG.35, EPE.39 Ligand excluded by PLIP EPE.29: 7 residues within 4Å: Chain C: G.193, T.195, N.196 Chain D: R.20 Chain F: D.143, Y.147, L.149 Ligand excluded by PLIP EPE.39: 10 residues within 4Å: Chain C: E.30, N.31, V.32, K.314 Chain D: E.30, N.31, V.32, K.314 Ligands: MG.24, EPE.28 Ligand excluded by PLIP EPE.40: 7 residues within 4Å: Chain C: R.20 Chain D: G.193, T.195, N.196 Chain G: D.143, Y.147, L.149 Ligand excluded by PLIP EPE.50: 10 residues within 4Å: Chain E: E.30, N.31, V.32, K.314 Chain G: E.30, N.31, V.32, K.314 Ligands: MG.68, EPE.72 Ligand excluded by PLIP EPE.51: 7 residues within 4Å: Chain C: D.143, Y.147, L.149 Chain E: G.193, T.195, N.196 Chain G: R.20 Ligand excluded by PLIP EPE.61: 10 residues within 4Å: Chain F: E.30, N.31, V.32, K.314 Chain H: E.30, N.31, V.32, K.314 Ligands: MG.79, EPE.83 Ligand excluded by PLIP EPE.62: 7 residues within 4Å: Chain A: D.143, Y.147, L.149 Chain F: G.193, T.195, N.196 Chain H: R.20 Ligand excluded by PLIP EPE.72: 10 residues within 4Å: Chain E: E.30, N.31, V.32, K.314 Chain G: E.30, N.31, V.32, K.314 Ligands: MG.46, EPE.50 Ligand excluded by PLIP EPE.73: 7 residues within 4Å: Chain B: D.143, Y.147, L.149 Chain E: R.20 Chain G: G.193, T.195, N.196 Ligand excluded by PLIP EPE.83: 10 residues within 4Å: Chain F: E.30, N.31, V.32, K.314 Chain H: E.30, N.31, V.32, K.314 Ligands: MG.57, EPE.61 Ligand excluded by PLIP EPE.84: 7 residues within 4Å: Chain D: D.143, Y.147, L.149 Chain F: R.20 Chain H: G.193, T.195, N.196 Ligand excluded by PLIP

32 x PE5: 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL(Non-covalent)

PE5.8: 7 residues within 4Å: Chain A: E.190, S.191 Chain B: Y.10, P.11, Y.12, R.14 Chain E: D.151 Ligand excluded by PLIP PE5.9: 5 residues within 4Å: Chain A: I.141, L.142, L.149, V.152 Ligands: PE5.10 Ligand excluded by PLIP PE5.10: 4 residues within 4Å: Chain A: D.97, V.152, D.155 Ligands: PE5.9 Ligand excluded by PLIP PE5.11: 5 residues within 4Å: Chain A: A.99, E.100, Y.102, N.103, P.104 Ligand excluded by PLIP PE5.19: 7 residues within 4Å: Chain A: Y.10, P.11, Y.12, R.14 Chain B: E.190, S.191 Chain H: D.151 Ligand excluded by PLIP PE5.20: 5 residues within 4Å: Chain B: I.141, L.142, L.149, V.152 Ligands: PE5.21 Ligand excluded by PLIP PE5.21: 4 residues within 4Å: Chain B: D.97, V.152, D.155 Ligands: PE5.20 Ligand excluded by PLIP PE5.22: 5 residues within 4Å: Chain B: A.99, E.100, Y.102, N.103, P.104 Ligand excluded by PLIP PE5.30: 7 residues within 4Å: Chain C: E.190, S.191 Chain D: Y.10, P.11, Y.12, R.14 Chain F: D.151 Ligand excluded by PLIP PE5.31: 5 residues within 4Å: Chain C: I.141, L.142, L.149, V.152 Ligands: PE5.32 Ligand excluded by PLIP PE5.32: 4 residues within 4Å: Chain C: D.97, V.152, D.155 Ligands: PE5.31 Ligand excluded by PLIP PE5.33: 5 residues within 4Å: Chain C: A.99, E.100, Y.102, N.103, P.104 Ligand excluded by PLIP PE5.41: 7 residues within 4Å: Chain C: Y.10, P.11, Y.12, R.14 Chain D: E.190, S.191 Chain G: D.151 Ligand excluded by PLIP PE5.42: 5 residues within 4Å: Chain D: I.141, L.142, L.149, V.152 Ligands: PE5.43 Ligand excluded by PLIP PE5.43: 4 residues within 4Å: Chain D: D.97, V.152, D.155 Ligands: PE5.42 Ligand excluded by PLIP PE5.44: 5 residues within 4Å: Chain D: A.99, E.100, Y.102, N.103, P.104 Ligand excluded by PLIP PE5.52: 7 residues within 4Å: Chain C: D.151 Chain E: E.190, S.191 Chain G: Y.10, P.11, Y.12, R.14 Ligand excluded by PLIP PE5.53: 5 residues within 4Å: Chain E: I.141, L.142, L.149, V.152 Ligands: PE5.54 Ligand excluded by PLIP PE5.54: 4 residues within 4Å: Chain E: D.97, V.152, D.155 Ligands: PE5.53 Ligand excluded by PLIP PE5.55: 5 residues within 4Å: Chain E: A.99, E.100, Y.102, N.103, P.104 Ligand excluded by PLIP PE5.63: 7 residues within 4Å: Chain A: D.151 Chain F: E.190, S.191 Chain H: Y.10, P.11, Y.12, R.14 Ligand excluded by PLIP PE5.64: 5 residues within 4Å: Chain F: I.141, L.142, L.149, V.152 Ligands: PE5.65 Ligand excluded by PLIP PE5.65: 4 residues within 4Å: Chain F: D.97, V.152, D.155 Ligands: PE5.64 Ligand excluded by PLIP PE5.66: 5 residues within 4Å: Chain F: A.99, E.100, Y.102, N.103, P.104 Ligand excluded by PLIP PE5.74: 7 residues within 4Å: Chain B: D.151 Chain E: Y.10, P.11, Y.12, R.14 Chain G: E.190, S.191 Ligand excluded by PLIP PE5.75: 5 residues within 4Å: Chain G: I.141, L.142, L.149, V.152 Ligands: PE5.76 Ligand excluded by PLIP PE5.76: 4 residues within 4Å: Chain G: D.97, V.152, D.155 Ligands: PE5.75 Ligand excluded by PLIP PE5.77: 5 residues within 4Å: Chain G: A.99, E.100, Y.102, N.103, P.104 Ligand excluded by PLIP PE5.85: 7 residues within 4Å: Chain D: D.151 Chain F: Y.10, P.11, Y.12, R.14 Chain H: E.190, S.191 Ligand excluded by PLIP PE5.86: 5 residues within 4Å: Chain H: I.141, L.142, L.149, V.152 Ligands: PE5.87 Ligand excluded by PLIP PE5.87: 4 residues within 4Å: Chain H: D.97, V.152, D.155 Ligands: PE5.86 Ligand excluded by PLIP PE5.88: 5 residues within 4Å: Chain H: A.99, E.100, Y.102, N.103, P.104 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Heinemann, I.U. et al., Structure of the heme biosynthetic Pseudomonas aeruginosa porphobilinogen synthase in complex with the antibiotic alaremycin. Antimicrob. Agents Chemother. (2010)

Release Date

2009-10-27

Peptides

DELTA-AMINOLEVULINIC ACID DEHYDRATASE: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

DELTA-AMINOLEVULINIC ACID DEHYDRATASE

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