SMTL ID : 8awy.1

Millisecond cryo-trapping by the spitrobot crystal plunger, Serial measurement Xylose Isomerase with 2,3-butanediol at 50ms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

12 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 Ligands: BU9.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 MG.2: 4 residues within 4Å: Chain A: H.54, D.57, N.92, F.94 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.54, A:H.54, H2O.6 MG.4: 4 residues within 4Å: Chain A: E.207, R.208, P.209, E.210 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.210, H2O.3, H2O.17, H2O.18, H2O.18 MG.5: 5 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 Ligands: BU9.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 MG.6: 4 residues within 4Å: Chain B: H.54, D.57, N.92, F.94 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.54, B:H.54, H2O.25 MG.8: 4 residues within 4Å: Chain B: E.207, R.208, P.209, E.210 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.210, H2O.21, H2O.36, H2O.36, H2O.37 MG.9: 5 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 Ligands: BU9.11 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 MG.10: 4 residues within 4Å: Chain C: H.54, D.57, N.92, F.94 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.54, C:H.54, H2O.43 MG.12: 4 residues within 4Å: Chain C: E.207, R.208, P.209, E.210 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.210, H2O.40, H2O.55, H2O.55, H2O.55 MG.13: 5 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 Ligands: BU9.15 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287 MG.14: 4 residues within 4Å: Chain D: H.54, D.57, N.92, F.94 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.54, D:H.54, H2O.62 MG.16: 4 residues within 4Å: Chain D: E.207, R.208, P.209, E.210 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.210, H2O.59, H2O.73, H2O.74, H2O.74

4 x BU9: Meso-2,3-Butanediol(Non-covalent)

BU9.3: 10 residues within 4Å: Chain A: W.16, H.54, T.90, F.94, V.135, W.137, E.181, D.245, D.287 Ligands: MG.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.90, A:V.135 Water bridges: A:T.90, A:T.90, A:N.215, A:D.245 BU9.7: 10 residues within 4Å: Chain B: W.16, H.54, T.90, F.94, V.135, W.137, E.181, D.245, D.287 Ligands: MG.5 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:T.90, B:V.135 Water bridges: B:T.90, B:T.90, B:N.215, B:D.245 BU9.11: 10 residues within 4Å: Chain C: W.16, H.54, T.90, F.94, V.135, W.137, E.181, D.245, D.287 Ligands: MG.9 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:T.90, C:V.135 Water bridges: C:H.54, C:T.90, C:N.215, C:D.245 BU9.15: 10 residues within 4Å: Chain D: W.16, H.54, T.90, F.94, V.135, W.137, E.181, D.245, D.287 Ligands: MG.13 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:T.90, D:V.135 Water bridges: D:H.54, D:T.90, D:N.215, D:D.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mehrabi, P. et al., Millisecond cryo-trapping by the spitrobot crystal plunger simplifies time-resolved crystallography. Nat Commun (2023)

Release Date

2023-05-24

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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