SMTL ID : 1e51.1

Crystal structure of native human erythrocyte 5-aminolaevulinic acid dehydratase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.83 Å

Oligo State

homo-octamer

Ligands

4 x PBG: 3-[5-(AMINOMETHYL)-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC ACID(Covalent)

PBG.1: 14 residues within 4Å: Chain A: C.124, S.168, K.199, Y.205, F.208, R.209, R.221, Q.225, K.252, Y.276, V.278, S.279, Y.318 Ligands: ZN.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.205, A:F.208, A:F.208 Hydrogen bonds: A:S.168, A:S.168, A:S.168, A:K.199, A:Q.225, A:S.279, A:Y.318, A:Y.318 Salt bridges: A:K.199, A:R.209, A:R.221, A:K.252 pi-Stacking: A:F.208 pi-Cation interactions: A:K.199 PBG.5: 14 residues within 4Å: Chain C: C.124, S.168, K.199, Y.205, F.208, R.209, R.221, Q.225, K.252, Y.276, V.278, S.279, Y.318 Ligands: ZN.6 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:Y.205, C:F.208, C:F.208 Hydrogen bonds: C:S.168, C:S.168, C:S.168, C:K.199, C:Q.225, C:S.279, C:Y.318, C:Y.318 Salt bridges: C:K.199, C:R.209, C:R.221, C:K.252 pi-Stacking: C:F.208 pi-Cation interactions: C:K.199 PBG.9: 14 residues within 4Å: Chain E: C.124, S.168, K.199, Y.205, F.208, R.209, R.221, Q.225, K.252, Y.276, V.278, S.279, Y.318 Ligands: ZN.10 17 PLIP interactions: 17 interactions with chain E Hydrophobic interactions: E:Y.205, E:F.208, E:F.208 Hydrogen bonds: E:S.168, E:S.168, E:S.168, E:K.199, E:Q.225, E:S.279, E:Y.318, E:Y.318 Salt bridges: E:K.199, E:R.209, E:R.221, E:K.252 pi-Stacking: E:F.208 pi-Cation interactions: E:K.199 PBG.13: 14 residues within 4Å: Chain G: C.124, S.168, K.199, Y.205, F.208, R.209, R.221, Q.225, K.252, Y.276, V.278, S.279, Y.318 Ligands: ZN.14 17 PLIP interactions: 17 interactions with chain G Hydrophobic interactions: G:Y.205, G:F.208, G:F.208 Hydrogen bonds: G:S.168, G:S.168, G:S.168, G:K.199, G:Q.225, G:S.279, G:Y.318, G:Y.318 Salt bridges: G:K.199, G:R.209, G:R.221, G:K.252 pi-Stacking: G:F.208 pi-Cation interactions: G:K.199

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.122, C.124, C.132 Ligands: PBG.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.122, A:C.124, A:C.132 ZN.6: 4 residues within 4Å: Chain C: C.122, C.124, C.132 Ligands: PBG.5 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.122, C:C.124, C:C.132 ZN.10: 4 residues within 4Å: Chain E: C.122, C.124, C.132 Ligands: PBG.9 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.122, E:C.124, E:C.132 ZN.14: 4 residues within 4Å: Chain G: C.122, C.124, C.132 Ligands: PBG.13 3 PLIP interactions: 3 interactions with chain G Metal complexes: G:C.122, G:C.124, G:C.132

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

SO4.3: 3 residues within 4Å: Chain A: P.14, R.17 Chain B: R.222 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.17, B:R.222 SO4.4: 2 residues within 4Å: Chain B: P.14, R.17 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.17 SO4.7: 3 residues within 4Å: Chain C: P.14, R.17 Chain D: R.222 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:R.17, D:R.222 SO4.8: 2 residues within 4Å: Chain D: P.14, R.17 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.17 SO4.11: 3 residues within 4Å: Chain E: P.14, R.17 Chain F: R.222 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Salt bridges: E:R.17, F:R.222 SO4.12: 2 residues within 4Å: Chain F: P.14, R.17 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.17 SO4.15: 3 residues within 4Å: Chain G: P.14, R.17 Chain H: R.222 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Salt bridges: H:R.222, G:R.17 SO4.16: 2 residues within 4Å: Chain H: P.14, R.17 1 PLIP interactions: 1 interactions with chain H Salt bridges: H:R.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mills-Davies, N.L. et al., The Crystal Structure of Human Ala-Dehydratase. To be Published

Release Date

2001-07-12

Peptides

DELTA-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

DELTA-AMINOLEVULINIC ACID DEHYDRATASE

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