SMTL ID : 1b4k.1

High resolution crystal structure of a MG2-dependent 5-aminolevulinic acid dehydratase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

homo-octamer

Ligands

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

SO4.1: 8 residues within 4Å: Chain A: D.131, K.205, Y.211, F.214, R.215, K.229, Q.233 Ligands: SHF.3 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:D.131, A:Q.233 Water bridges: A:K.205, A:K.205, A:K.229, A:K.229 Salt bridges: A:K.205, A:R.215, A:K.229, A:K.260 SO4.4: 5 residues within 4Å: Chain B: K.205, Y.211, R.215, Q.233 Ligands: SHF.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.233 Water bridges: B:S.175, B:K.205 Salt bridges: B:K.205, B:R.215 SO4.6: 8 residues within 4Å: Chain C: D.131, K.205, Y.211, F.214, R.215, K.229, Q.233 Ligands: SHF.8 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:D.131, C:Q.233 Water bridges: C:K.205, C:K.205, C:K.229, C:K.229 Salt bridges: C:K.205, C:R.215, C:K.229, C:K.260 SO4.9: 5 residues within 4Å: Chain D: K.205, Y.211, R.215, Q.233 Ligands: SHF.10 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:Q.233 Water bridges: D:S.175, D:K.205 Salt bridges: D:K.205, D:R.215 SO4.11: 8 residues within 4Å: Chain E: D.131, K.205, Y.211, F.214, R.215, K.229, Q.233 Ligands: SHF.13 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:D.131, E:Q.233 Water bridges: E:K.205, E:K.205, E:K.229, E:K.229 Salt bridges: E:K.205, E:R.215, E:K.229, E:K.260 SO4.14: 5 residues within 4Å: Chain F: K.205, Y.211, R.215, Q.233 Ligands: SHF.15 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:Q.233 Water bridges: F:S.175, F:K.205 Salt bridges: F:K.205, F:R.215 SO4.16: 8 residues within 4Å: Chain G: D.131, K.205, Y.211, F.214, R.215, K.229, Q.233 Ligands: SHF.18 10 PLIP interactions: 10 interactions with chain G Hydrogen bonds: G:D.131, G:Q.233 Water bridges: G:K.205, G:K.205, G:K.229, G:K.229 Salt bridges: G:K.205, G:R.215, G:K.229, G:K.260 SO4.19: 5 residues within 4Å: Chain H: K.205, Y.211, R.215, Q.233 Ligands: SHF.20 5 PLIP interactions: 5 interactions with chain H Hydrogen bonds: H:Q.233 Water bridges: H:S.175, H:K.205 Salt bridges: H:K.205, H:R.215

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 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.1, H2O.1, H2O.1, H2O.1, H2O.1 MG.7: 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.23, H2O.23, H2O.23, H2O.23, H2O.23 MG.12: 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.45, H2O.45, H2O.45, H2O.45, H2O.45 MG.17: 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.67, H2O.67, H2O.67, H2O.67, H2O.67

8 x SHF: LAEVULINIC ACID(Covalent)

SHF.3: 10 residues within 4Å: Chain A: Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: SO4.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.202, A:F.214, A:F.214, A:K.260, A:Y.283 Hydrogen bonds: A:Y.283, A:S.286, A:Y.324 Salt bridges: A:K.260 SHF.5: 10 residues within 4Å: Chain B: S.175, Y.202, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: SO4.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.202, B:F.214, B:F.214, B:K.260, B:Y.283 Hydrogen bonds: B:S.286, B:Y.324 Salt bridges: B:K.260 SHF.8: 10 residues within 4Å: Chain C: Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: SO4.6 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.202, C:F.214, C:F.214, C:K.260, C:Y.283 Hydrogen bonds: C:Y.283, C:S.286, C:Y.324 Salt bridges: C:K.260 SHF.10: 10 residues within 4Å: Chain D: S.175, Y.202, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: SO4.9 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.202, D:F.214, D:F.214, D:K.260, D:Y.283 Hydrogen bonds: D:S.286, D:Y.324 Salt bridges: D:K.260 SHF.13: 10 residues within 4Å: Chain E: Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: SO4.11 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:Y.202, E:F.214, E:F.214, E:K.260, E:Y.283 Hydrogen bonds: E:Y.283, E:S.286, E:Y.324 Salt bridges: E:K.260 SHF.15: 10 residues within 4Å: Chain F: S.175, Y.202, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: SO4.14 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:Y.202, F:F.214, F:F.214, F:K.260, F:Y.283 Hydrogen bonds: F:S.286, F:Y.324 Salt bridges: F:K.260 SHF.18: 10 residues within 4Å: Chain G: Y.202, K.205, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: SO4.16 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:Y.202, G:F.214, G:F.214, G:K.260, G:Y.283 Hydrogen bonds: G:Y.283, G:S.286, G:Y.324 Salt bridges: G:K.260 SHF.20: 10 residues within 4Å: Chain H: S.175, Y.202, Y.211, F.214, K.260, Y.283, V.285, S.286, Y.324 Ligands: SO4.19 8 PLIP interactions: 8 interactions with chain H Hydrophobic interactions: H:Y.202, H:F.214, H:F.214, H:K.260, H:Y.283 Hydrogen bonds: H:S.286, H:Y.324 Salt bridges: H:K.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frankenberg, N. et al., High resolution crystal structure of a Mg2+-dependent porphobilinogen synthase. J.Mol.Biol. (1999)

Release Date

1999-07-13

Peptides

PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE): 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

PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE)

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