SMTL ID : 3cwh.1

D-xylose Isomerase in complex with linear product, per-deuterated xylulose

Coordinates

PDB Format

Method

NEUTRON DIFFRACTION 2.20 Å

Oligo State

homo-tetramer

Ligands

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

XUL.1: 20 residues within 4Å: Chain A: W.16, H.54, T.90, F.94, V.135, W.137, E.181, K.183, N.215, E.217, H.220, D.245, D.255, D.257, D.287, K.289 Chain C: F.26 Ligands: MG.2, MG.3, OH.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:W.16, A:H.54, A:E.181, A:K.183, A:H.220 Water bridges: A:T.91, A:W.137 XUL.5: 20 residues within 4Å: Chain B: W.16, H.54, T.90, F.94, V.135, W.137, E.181, K.183, N.215, E.217, H.220, D.245, D.255, D.257, D.287, K.289 Chain D: F.26 Ligands: MG.6, MG.7, OH.8 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:W.16, B:H.54, B:E.181, B:K.183, B:H.220 Water bridges: B:T.91, B:W.137 XUL.9: 20 residues within 4Å: Chain A: F.26 Chain C: W.16, H.54, T.90, F.94, V.135, W.137, E.181, K.183, N.215, E.217, H.220, D.245, D.255, D.257, D.287, K.289 Ligands: MG.10, MG.11, OH.12 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:W.16, C:H.54, C:E.181, C:K.183, C:H.220 Water bridges: C:T.91, C:W.137 XUL.13: 20 residues within 4Å: Chain B: F.26 Chain D: W.16, H.54, T.90, F.94, V.135, W.137, E.181, K.183, N.215, E.217, H.220, D.245, D.255, D.257, D.287, K.289 Ligands: MG.14, MG.15, OH.16 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:W.16, D:H.54, D:E.181, D:K.183, D:H.220 Water bridges: D:T.91, D:W.137

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 8 residues within 4Å: Chain A: K.183, E.217, H.220, N.247, D.255, D.257 Ligands: XUL.1, OH.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:E.217, A:H.220, A:D.255, A:D.257, OH.4 MG.3: 7 residues within 4Å: Chain A: E.181, E.217, H.220, D.245, D.287 Ligands: XUL.1, OH.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 MG.6: 8 residues within 4Å: Chain B: K.183, E.217, H.220, N.247, D.255, D.257 Ligands: XUL.5, OH.8 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:E.217, B:H.220, B:D.255, B:D.257, OH.8 MG.7: 7 residues within 4Å: Chain B: E.181, E.217, H.220, D.245, D.287 Ligands: XUL.5, OH.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 MG.10: 8 residues within 4Å: Chain C: K.183, E.217, H.220, N.247, D.255, D.257 Ligands: XUL.9, OH.12 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:E.217, C:H.220, C:D.255, C:D.257, OH.12 MG.11: 7 residues within 4Å: Chain C: E.181, E.217, H.220, D.245, D.287 Ligands: XUL.9, OH.12 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 MG.14: 8 residues within 4Å: Chain D: K.183, E.217, H.220, N.247, D.255, D.257 Ligands: XUL.13, OH.16 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 MG.15: 7 residues within 4Å: Chain D: E.181, E.217, H.220, D.245, D.287 Ligands: XUL.13, OH.16 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287

4 x OH: HYDROXIDE ION(Non-covalent)

OH.4: 10 residues within 4Å: Chain A: E.217, H.220, N.247, D.255, D.257, D.287, K.289 Ligands: XUL.1, MG.2, MG.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.257 OH.8: 10 residues within 4Å: Chain B: E.217, H.220, N.247, D.255, D.257, D.287, K.289 Ligands: XUL.5, MG.6, MG.7 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.220 OH.12: 10 residues within 4Å: Chain C: E.217, H.220, N.247, D.255, D.257, D.287, K.289 Ligands: XUL.9, MG.10, MG.11 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.257 OH.16: 10 residues within 4Å: Chain D: E.217, H.220, N.247, D.255, D.257, D.287, K.289 Ligands: XUL.13, MG.14, MG.15 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.257

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kovalevsky, A.Y. et al., Hydrogen location in stages of an enzyme-catalyzed reaction: time-of-flight neutron structure of D-xylose isomerase with bound D-xylulose. Biochemistry (2008)

Release Date

2008-08-05

Peptides

Xylose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Xylose isomerase

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