SMTL ID : 5oyn.1

Crystal structure of D-xylonate dehydratase in holo-form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.101, D.138, K.139, T.215, E.472 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.101, A:D.138, A:E.472, H2O.1 MG.3: 5 residues within 4Å: Chain B: E.101, D.138, K.139, T.215, E.472 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.101, B:D.138, B:E.472, H2O.4 MG.5: 5 residues within 4Å: Chain C: E.101, D.138, K.139, T.215, E.472 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.101, C:D.138, C:E.472, H2O.6 MG.7: 4 residues within 4Å: Chain D: E.101, D.138, K.139, E.472 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.101, D:D.138, D:E.472, D:E.472, H2O.9

4 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.2: 9 residues within 4Å: Chain A: C.69, F.100, N.102, C.137, D.138, H.209, C.210, A.216 Chain B: R.39 3 PLIP interactions: 3 interactions with chain A, Metal complexes: A:C.69, A:C.137, A:C.210 FES.4: 8 residues within 4Å: Chain A: R.39 Chain B: C.69, N.102, C.137, D.138, H.209, C.210, A.216 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.69, B:C.137, B:C.210 FES.6: 9 residues within 4Å: Chain C: C.69, E.101, N.102, C.137, D.138, H.209, C.210, A.216 Chain D: R.39 3 PLIP interactions: 3 interactions with chain C, Metal complexes: C:C.69, C:C.137, C:C.210 FES.8: 8 residues within 4Å: Chain C: R.39 Chain D: C.69, N.102, C.137, D.138, H.209, C.210, A.216 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:C.69, D:C.137, D:C.210, H2O.11

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rahman, M.M. et al., The crystal structure of D-xylonate dehydratase reveals functional features of enzymes from the Ilv/ED dehydratase family. Sci Rep (2018)

Release Date

2018-01-24

Peptides

Dehydratase, IlvD/Edd family: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Dehydratase, IlvD/Edd family