SMTL ID : 9g6m.1

Xylose Isomerase collected at 30C using time-resolved serial synchrotron crystallography with Glucose at 60 seconds

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.1: 14 residues within 4Å: Chain A: W.16, H.54, T.90, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Chain B: F.26 Ligands: GLO.2, MG.3, MG.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.90, A:D.287 Water bridges: A:W.16, A:N.215 Salt bridges: A:H.54 GLC.6: 14 residues within 4Å: Chain A: F.26 Chain B: W.16, H.54, T.90, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: GLO.7, MG.8, MG.9 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.90, B:D.287 Water bridges: B:W.16, B:N.215 Salt bridges: B:H.54 GLC.11: 14 residues within 4Å: Chain C: W.16, H.54, T.90, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Chain D: F.26 Ligands: GLO.12, MG.13, MG.14 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.287 Water bridges: C:W.16, C:N.215, C:D.245, C:D.287 Salt bridges: C:H.54 GLC.16: 14 residues within 4Å: Chain C: F.26 Chain D: W.16, H.54, T.90, F.94, W.137, E.181, E.217, H.220, D.245, D.287 Ligands: GLO.17, MG.18, MG.19 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:D.287 Water bridges: D:W.16, D:N.215, D:D.245, D:D.287 Salt bridges: D:H.54

4 x GLO: D-glucose(Non-covalent)

GLO.2: 18 residues within 4Å: Chain A: W.16, H.54, M.88, T.90, V.135, W.137, E.181, K.183, E.217, H.220, D.245, D.255, D.287 Chain B: F.26 Ligands: GLC.1, MG.3, MG.4, MG.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:W.16, A:T.90, A:E.181, A:H.220 Water bridges: A:N.215 GLO.7: 18 residues within 4Å: Chain A: F.26 Chain B: W.16, H.54, M.88, T.90, V.135, W.137, E.181, K.183, E.217, H.220, D.245, D.255, D.287 Ligands: GLC.6, MG.8, MG.9, MG.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:W.16, B:T.90, B:E.181, B:H.220 Water bridges: B:N.215 GLO.12: 18 residues within 4Å: Chain C: W.16, H.54, M.88, T.90, V.135, W.137, E.181, K.183, E.217, H.220, D.245, D.255, D.287 Chain D: F.26 Ligands: GLC.11, MG.13, MG.14, MG.15 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:W.16, C:E.181, C:E.181, C:H.220 Water bridges: C:N.215, C:D.287, C:D.287 GLO.17: 18 residues within 4Å: Chain C: F.26 Chain D: W.16, H.54, M.88, T.90, V.135, W.137, E.181, K.183, E.217, H.220, D.245, D.255, D.287 Ligands: GLC.16, MG.18, MG.19, MG.20 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:W.16, D:E.181, D:E.181, D:H.220 Water bridges: D:N.215, D:D.287, D:D.287

12 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 7 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 Ligands: GLC.1, GLO.2, MG.4 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287, H2O.1, H2O.1 MG.4: 9 residues within 4Å: Chain A: E.217, H.220, D.255, D.257, D.287 Ligands: GLC.1, GLO.2, MG.3, MG.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.217, A:E.217, A:H.220, H2O.1, H2O.1 MG.5: 7 residues within 4Å: Chain A: E.217, H.220, N.247, D.255, D.257 Ligands: GLO.2, MG.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.217, A:H.220, A:D.255, A:D.257, H2O.1 MG.8: 7 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 Ligands: GLC.6, GLO.7, MG.9 6 PLIP interactions: 4 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287, H2O.12, H2O.13 MG.9: 9 residues within 4Å: Chain B: E.217, H.220, D.255, D.257, D.287 Ligands: GLC.6, GLO.7, MG.8, MG.10 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.217, B:E.217, B:H.220, H2O.13, H2O.13 MG.10: 7 residues within 4Å: Chain B: E.217, H.220, N.247, D.255, D.257 Ligands: GLO.7, MG.9 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.217, B:H.220, B:D.255, B:D.257, H2O.13 MG.13: 7 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 Ligands: GLC.11, GLO.12, MG.14 6 PLIP interactions: 4 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287, H2O.24, H2O.24 MG.14: 9 residues within 4Å: Chain C: E.217, H.220, D.255, D.257, D.287 Ligands: GLC.11, GLO.12, MG.13, MG.15 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:E.217, C:E.217, C:H.220, H2O.24, H2O.24 MG.15: 7 residues within 4Å: Chain C: E.217, H.220, N.247, D.255, D.257 Ligands: GLO.12, MG.14 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.217, C:H.220, C:D.255, C:D.257, H2O.24 MG.18: 7 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 Ligands: GLC.16, GLO.17, MG.19 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287, H2O.35, H2O.36 MG.19: 9 residues within 4Å: Chain D: E.217, H.220, D.255, D.257, D.287 Ligands: GLC.16, GLO.17, MG.18, MG.20 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.217, D:E.217, D:H.220, H2O.36, H2O.36 MG.20: 7 residues within 4Å: Chain D: E.217, H.220, N.247, D.255, D.257 Ligands: GLO.17, MG.19 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.217, D:H.220, D:D.255, D:D.257, H2O.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schulz, E.C. et al., Probing the modulation of enzyme kinetics by multi-temperature, time-resolved serial crystallography. Nat Commun (2025)

Release Date

2025-07-30

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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