SMTL ID : 5hnr.1

The X-ray structure of octameric human native 5-aminolaevulinic acid dehydratase.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.83 Å

Oligo State

homo-octamer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.122, C.124, C.132, S.168 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.122, A:C.124, A:C.132, H2O.3 ZN.5: 4 residues within 4Å: Chain C: C.122, C.124, C.132, S.168 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.122, C:C.124, C:C.132, H2O.7 ZN.9: 4 residues within 4Å: Chain E: C.122, C.124, C.132, S.168 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:C.122, E:C.124, E:C.132, H2O.12 ZN.13: 4 residues within 4Å: Chain G: C.122, C.124, C.132, S.168 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:C.122, G:C.124, G:C.132, H2O.17

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

SO4.2: 3 residues within 4Å: Chain A: P.14, R.17 Chain B: R.222 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.222, A:R.17 Hydrogen bonds: A:P.14 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 SO4.6: 3 residues within 4Å: Chain C: P.14, R.17 Chain D: R.222 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:P.14 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 SO4.10: 3 residues within 4Å: Chain E: P.14, R.17 Chain F: R.222 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain E Salt bridges: F:R.222, E:R.17 Hydrogen bonds: E:P.14 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 SO4.14: 3 residues within 4Å: Chain G: P.14, R.17 Chain H: R.222 3 PLIP interactions: 2 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:P.14 Salt bridges: G:R.17, H:R.222 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

4 x DAV: DELTA-AMINO VALERIC ACID(Covalent)

DAV.3: 10 residues within 4Å: Chain A: D.120, S.168, K.199, Y.205, F.208, K.252, Y.276, V.278, S.279, Y.318 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.205, A:F.208, A:F.208, A:K.252, A:V.278 Hydrogen bonds: A:S.168, A:S.168, A:K.199, A:Y.205, A:F.208, A:Y.276, A:S.279, A:Y.318 Salt bridges: A:K.252 DAV.7: 10 residues within 4Å: Chain C: D.120, S.168, K.199, Y.205, F.208, K.252, Y.276, V.278, S.279, Y.318 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:Y.205, C:F.208, C:F.208, C:K.252, C:V.278 Hydrogen bonds: C:S.168, C:S.168, C:K.199, C:Y.205, C:F.208, C:Y.276, C:S.279, C:Y.318 Salt bridges: C:K.252 DAV.11: 10 residues within 4Å: Chain E: D.120, S.168, K.199, Y.205, F.208, K.252, Y.276, V.278, S.279, Y.318 14 PLIP interactions: 14 interactions with chain E Hydrophobic interactions: E:Y.205, E:F.208, E:F.208, E:K.252, E:V.278 Hydrogen bonds: E:S.168, E:S.168, E:K.199, E:Y.205, E:F.208, E:Y.276, E:S.279, E:Y.318 Salt bridges: E:K.252 DAV.15: 10 residues within 4Å: Chain G: D.120, S.168, K.199, Y.205, F.208, K.252, Y.276, V.278, S.279, Y.318 14 PLIP interactions: 14 interactions with chain G Hydrophobic interactions: G:Y.205, G:F.208, G:F.208, G:K.252, G:V.278 Hydrogen bonds: G:S.168, G:S.168, G:K.199, G:Y.205, G:F.208, G:Y.276, G:S.279, G:Y.318 Salt bridges: G:K.252

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mills-Davies, N. et al., Structural studies of substrate and product complexes of 5-aminolaevulinic acid dehydratase from humans, Escherichia coli and the hyperthermophile Pyrobaculum calidifontis. Acta Crystallogr D Struct Biol (2017)

Release Date

2016-01-27

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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