SMTL ID : 6n99.1

Xylose isomerase 2F1 variant from Streptomyces sp. F-1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

5 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.217, H.220, D.255, D.257 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.217, A:D.255, A:D.257 MG.2: 5 residues within 4Å: Chain B: K.183, E.217, H.220, D.255, D.257 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.220, B:D.255, B:D.257 MG.3: 6 residues within 4Å: Chain B: M.88, E.181, N.215, D.245, H.285, D.287 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.181, B:D.245 MG.7: 5 residues within 4Å: Chain C: K.183, E.217, H.220, D.255, D.257 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:E.217, C:D.255, C:D.257 MG.8: 4 residues within 4Å: Chain D: E.217, H.220, D.255, D.257 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:E.217, D:H.220, D:D.255, D:D.255, D:D.257

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

SO4.4: 1 residues within 4Å: Chain B: R.152 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.152 SO4.5: 3 residues within 4Å: Chain B: R.23, D.28, A.29 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.29 Salt bridges: B:R.23

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.6: 1 residues within 4Å: Chain B: R.121 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Miyamoto, R.Y. et al., Crystal structure of a novel xylose isomerase from Streptomyces sp. F-1 revealed the presence of unique features that differ from conventional classes. Biochim Biophys Acta Gen Subj (2020)

Release Date

2019-12-04

Peptides

Xylose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Xylose isomerase