SMTL ID : 2itm.1

Crystal structure of the E. coli xylulose kinase complexed with xylulose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x XUL: D-XYLULOSE(Non-covalent)

XUL.1: 7 residues within 4Å: Chain A: Q.76, M.77, H.78, W.96, D.233, N.234, M.288 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.77, A:H.78, A:H.78, A:N.234 XUL.10: 6 residues within 4Å: Chain B: M.77, H.78, W.96, D.233, N.234, M.288 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.77, B:H.78, B:N.234

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

SO4.2: 1 residues within 4Å: Chain A: R.196 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.196 SO4.11: 4 residues within 4Å: Chain B: G.254, T.255, G.394, G.395 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.255, B:T.255, B:G.395

12 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NH4.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NH4.5: 1 residues within 4Å: Chain A: N.97 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.35, A:N.97 Water bridges: A:R.35 NH4.6: 1 residues within 4Å: Chain A: D.197 No protein-ligand interaction detected (PLIP) NH4.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NH4.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NH4.9: 1 residues within 4Å: Chain A: V.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.33, A:V.33 NH4.12: 1 residues within 4Å: Chain B: R.137 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.137 NH4.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NH4.14: 1 residues within 4Å: Chain B: R.54 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.54 NH4.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) NH4.16: 1 residues within 4Å: Chain B: A.315 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Di Luccio, E. et al., Structural and kinetic studies of induced fit in xylulose kinase from Escherichia coli. J.Mol.Biol. (2007)

Release Date

2006-11-14

Peptides

Xylulose kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Xylulose kinase

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