SMTL ID : 1b4e.1

X-ray structure of 5-aminolevulinic acid dehydratase complexed with the inhibitor levulinic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

24 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: P.14, R.17 Chain G: K.216 Ligand excluded by PLIP SO4.2: 6 residues within 4Å: Chain A: R.225 Chain F: R.226 Chain G: R.256, R.259, G.304 Ligands: SO4.52 Ligand excluded by PLIP SO4.3: 6 residues within 4Å: Chain A: K.12, S.13, L.16 Chain E: K.106, P.110, D.159 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain B: P.14, R.17 Chain H: K.216 Ligand excluded by PLIP SO4.12: 6 residues within 4Å: Chain B: R.225 Chain E: R.226 Chain H: R.256, R.259, G.304 Ligands: SO4.42 Ligand excluded by PLIP SO4.13: 6 residues within 4Å: Chain B: K.12, S.13, L.16 Chain F: K.106, P.110, D.159 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: P.14, R.17 Chain E: K.216 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain C: R.225 Chain E: R.256, R.259, G.304 Chain G: R.226 Ligands: SO4.62 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain C: K.12, S.13, L.16 Chain H: K.106, P.110, D.159 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain D: P.14, R.17 Chain F: K.216 Ligand excluded by PLIP SO4.32: 6 residues within 4Å: Chain D: R.225 Chain F: R.256, R.259, G.304 Chain H: R.226 Ligands: SO4.72 Ligand excluded by PLIP SO4.33: 6 residues within 4Å: Chain D: K.12, S.13, L.16 Chain G: K.106, P.110, D.159 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain C: K.216 Chain E: P.14, R.17 Ligand excluded by PLIP SO4.42: 6 residues within 4Å: Chain B: R.226 Chain C: R.256, R.259, G.304 Chain E: R.225 Ligands: SO4.12 Ligand excluded by PLIP SO4.43: 6 residues within 4Å: Chain A: K.106, P.110, D.159 Chain E: K.12, S.13, L.16 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain D: K.216 Chain F: P.14, R.17 Ligand excluded by PLIP SO4.52: 6 residues within 4Å: Chain A: R.226 Chain D: R.256, R.259, G.304 Chain F: R.225 Ligands: SO4.2 Ligand excluded by PLIP SO4.53: 6 residues within 4Å: Chain B: K.106, P.110, D.159 Chain F: K.12, S.13, L.16 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain A: K.216 Chain G: P.14, R.17 Ligand excluded by PLIP SO4.62: 6 residues within 4Å: Chain A: R.256, R.259, G.304 Chain C: R.226 Chain G: R.225 Ligands: SO4.22 Ligand excluded by PLIP SO4.63: 6 residues within 4Å: Chain D: K.106, P.110, D.159 Chain G: K.12, S.13, L.16 Ligand excluded by PLIP SO4.71: 3 residues within 4Å: Chain B: K.216 Chain H: P.14, R.17 Ligand excluded by PLIP SO4.72: 6 residues within 4Å: Chain B: R.256, R.259, G.304 Chain D: R.226 Chain H: R.225 Ligands: SO4.32 Ligand excluded by PLIP SO4.73: 6 residues within 4Å: Chain C: K.106, P.110, D.159 Chain H: K.12, S.13, L.16 Ligand excluded by PLIP

24 x ZN: ZINC ION(Non-covalent)

ZN.4: 2 residues within 4Å: Chain A: E.39, H.83 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.39, A:E.39, A:H.83 ZN.5: 3 residues within 4Å: Chain A: C.119, C.121, C.129 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.119, A:C.121, A:C.129, H2O.15 ZN.6: 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.8, H2O.8, H2O.8, H2O.15, H2O.15 ZN.14: 2 residues within 4Å: Chain B: E.39, H.83 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:E.39, B:E.39, B:H.83 ZN.15: 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.29 ZN.16: 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.22, H2O.22, H2O.22, H2O.29, H2O.29 ZN.24: 2 residues within 4Å: Chain C: E.39, H.83 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.39, C:E.39, C:H.83 ZN.25: 3 residues within 4Å: Chain C: C.119, C.121, C.129 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.119, C:C.121, C:C.129, H2O.43 ZN.26: 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.37, H2O.37, H2O.37, H2O.43, H2O.43 ZN.34: 2 residues within 4Å: Chain D: E.39, H.83 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:E.39, D:E.39, D:H.83 ZN.35: 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.57 ZN.36: 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.51, H2O.51, H2O.51, H2O.58, H2O.58 ZN.44: 2 residues within 4Å: Chain E: E.39, H.83 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:E.39, E:E.39, E:H.83 ZN.45: 3 residues within 4Å: Chain E: C.119, C.121, C.129 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:C.119, E:C.121, E:C.129, H2O.72 ZN.46: 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.65, H2O.65, H2O.65, H2O.72, H2O.72 ZN.54: 2 residues within 4Å: Chain F: E.39, H.83 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:E.39, F:E.39, F:H.83 ZN.55: 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.86 ZN.56: 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.79, H2O.79, H2O.79, H2O.86, H2O.86 ZN.64: 2 residues within 4Å: Chain G: E.39, H.83 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:E.39, G:E.39, G:H.83 ZN.65: 3 residues within 4Å: Chain G: C.119, C.121, C.129 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:C.119, G:C.121, G:C.129, H2O.100 ZN.66: 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.94, H2O.94, H2O.94, H2O.100, H2O.100 ZN.74: 2 residues within 4Å: Chain H: E.39, H.83 3 PLIP interactions: 3 interactions with chain H Metal complexes: H:E.39, H:E.39, H:H.83 ZN.75: 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.115 ZN.76: 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.108, H2O.108, H2O.108, H2O.115, H2O.115

8 x SHF: LAEVULINIC ACID(Covalent)

SHF.7: 11 residues within 4Å: Chain A: F.78, Y.191, K.194, F.199, Y.200, F.203, K.246, Y.269, V.271, S.272, Y.311 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.78, A:Y.191, A:Y.200, A:F.203, A:F.203, A:F.203, A:K.246, A:Y.269 Hydrogen bonds: A:Y.200, A:S.272, A:Y.311 Salt bridges: A:K.246 SHF.17: 11 residues within 4Å: Chain B: F.78, Y.191, K.194, F.199, Y.200, F.203, K.246, Y.269, V.271, S.272, Y.311 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:F.78, B:Y.191, B:Y.200, B:F.203, B:F.203, B:F.203, B:K.246, B:Y.269 Hydrogen bonds: B:Y.200, B:S.272, B:Y.311 Salt bridges: B:K.246 SHF.27: 11 residues within 4Å: Chain C: F.78, Y.191, K.194, F.199, Y.200, F.203, K.246, Y.269, V.271, S.272, Y.311 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.78, C:Y.191, C:Y.200, C:F.203, C:F.203, C:F.203, C:K.246, C:Y.269 Hydrogen bonds: C:Y.200, C:S.272, C:Y.311 Salt bridges: C:K.246 SHF.37: 11 residues within 4Å: Chain D: F.78, Y.191, K.194, F.199, Y.200, F.203, K.246, Y.269, V.271, S.272, Y.311 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:F.78, D:Y.191, D:Y.200, D:F.203, D:F.203, D:F.203, D:K.246, D:Y.269 Hydrogen bonds: D:Y.200, D:S.272, D:Y.311 Salt bridges: D:K.246 SHF.47: 11 residues within 4Å: Chain E: F.78, Y.191, K.194, F.199, Y.200, F.203, K.246, Y.269, V.271, S.272, Y.311 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:F.78, E:Y.191, E:Y.200, E:F.203, E:F.203, E:F.203, E:K.246, E:Y.269 Hydrogen bonds: E:Y.200, E:S.272 Salt bridges: E:K.246 SHF.57: 11 residues within 4Å: Chain F: F.78, Y.191, K.194, F.199, Y.200, F.203, K.246, Y.269, V.271, S.272, Y.311 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:F.78, F:Y.191, F:Y.200, F:F.203, F:F.203, F:F.203, F:K.246, F:Y.269 Hydrogen bonds: F:Y.200, F:S.272 Salt bridges: F:K.246 SHF.67: 11 residues within 4Å: Chain G: F.78, Y.191, K.194, F.199, Y.200, F.203, K.246, Y.269, V.271, S.272, Y.311 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:F.78, G:Y.191, G:Y.200, G:F.203, G:F.203, G:F.203, G:K.246, G:Y.269 Hydrogen bonds: G:Y.200, G:S.272 Salt bridges: G:K.246 SHF.77: 11 residues within 4Å: Chain H: F.78, Y.191, K.194, F.199, Y.200, F.203, K.246, Y.269, V.271, S.272, Y.311 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:F.78, H:Y.191, H:Y.200, H:F.203, H:F.203, H:F.203, H:K.246, H:Y.269 Hydrogen bonds: H:Y.200, H:S.272 Salt bridges: H:K.246

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: G.249, E.274, I.278, S.296 Chain G: F.199, M.277 Ligands: GOL.68 Ligand excluded by PLIP GOL.9: 4 residues within 4Å: Chain A: E.21, L.294, E.295 Chain G: M.223 Ligand excluded by PLIP GOL.10: 4 residues within 4Å: Chain A: E.94, A.155, A.181, F.183 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain B: G.249, E.274, I.278, S.296 Chain H: F.199, M.277 Ligands: GOL.78 Ligand excluded by PLIP GOL.19: 4 residues within 4Å: Chain B: E.21, L.294, E.295 Chain H: M.223 Ligand excluded by PLIP GOL.20: 4 residues within 4Å: Chain B: E.94, A.155, A.181, F.183 Ligand excluded by PLIP GOL.28: 7 residues within 4Å: Chain C: G.249, E.274, I.278, S.296 Chain E: F.199, M.277 Ligands: GOL.48 Ligand excluded by PLIP GOL.29: 4 residues within 4Å: Chain C: E.21, L.294, E.295 Chain E: M.223 Ligand excluded by PLIP GOL.30: 4 residues within 4Å: Chain C: E.94, A.155, A.181, F.183 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain D: G.249, E.274, I.278, S.296 Chain F: F.199, M.277 Ligands: GOL.58 Ligand excluded by PLIP GOL.39: 4 residues within 4Å: Chain D: E.21, L.294, E.295 Chain F: M.223 Ligand excluded by PLIP GOL.40: 4 residues within 4Å: Chain D: E.94, A.155, A.181, F.183 Ligand excluded by PLIP GOL.48: 7 residues within 4Å: Chain C: F.199, M.277 Chain E: G.249, E.274, I.278, S.296 Ligands: GOL.28 Ligand excluded by PLIP GOL.49: 4 residues within 4Å: Chain C: M.223 Chain E: E.21, L.294, E.295 Ligand excluded by PLIP GOL.50: 4 residues within 4Å: Chain E: E.94, A.155, A.181, F.183 Ligand excluded by PLIP GOL.58: 7 residues within 4Å: Chain D: F.199, M.277 Chain F: G.249, E.274, I.278, S.296 Ligands: GOL.38 Ligand excluded by PLIP GOL.59: 4 residues within 4Å: Chain D: M.223 Chain F: E.21, L.294, E.295 Ligand excluded by PLIP GOL.60: 4 residues within 4Å: Chain F: E.94, A.155, A.181, F.183 Ligand excluded by PLIP GOL.68: 7 residues within 4Å: Chain A: F.199, M.277 Chain G: G.249, E.274, I.278, S.296 Ligands: GOL.8 Ligand excluded by PLIP GOL.69: 4 residues within 4Å: Chain A: M.223 Chain G: E.21, L.294, E.295 Ligand excluded by PLIP GOL.70: 4 residues within 4Å: Chain G: E.94, A.155, A.181, F.183 Ligand excluded by PLIP GOL.78: 7 residues within 4Å: Chain B: F.199, M.277 Chain H: G.249, E.274, I.278, S.296 Ligands: GOL.18 Ligand excluded by PLIP GOL.79: 4 residues within 4Å: Chain B: M.223 Chain H: E.21, L.294, E.295 Ligand excluded by PLIP GOL.80: 4 residues within 4Å: Chain H: E.94, A.155, A.181, F.183 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Erskine, P.T. et al., X-ray structure of 5-aminolevulinic acid dehydratase from Escherichia coli complexed with the inhibitor levulinic acid at 2.0 A resolution. Biochemistry (1999)

Release Date

1999-12-17

Peptides

PROTEIN (5-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

PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE)