SMTL ID : 8aw9.1

Xylose Isomerase in 75% relative humidity environment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.62 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 Ligands: GOL.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.181, A:E.217, A:D.245, A:D.287 MG.4: 5 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.181, B:E.217, B:D.245, B:D.287 MG.7: 5 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 Ligands: GOL.9 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.181, C:E.217, C:D.245, C:D.287 MG.10: 5 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.181, D:E.217, D:D.245, D:D.287

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: E.217, H.220, N.247, D.255, D.257 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.7 MN.5: 5 residues within 4Å: Chain B: E.217, H.220, N.247, D.255, D.257 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.15 MN.8: 5 residues within 4Å: Chain C: E.217, H.220, N.247, D.255, D.257 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.23 MN.11: 5 residues within 4Å: Chain D: E.217, H.220, N.247, D.255, D.257 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.31

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 8 residues within 4Å: Chain A: W.16, H.54, F.94, W.137, E.181, D.245, D.287 Ligands: MG.1 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.90, A:T.91 GOL.6: 8 residues within 4Å: Chain B: W.16, H.54, F.94, W.137, E.181, D.245, D.287 Ligands: MG.4 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.245 Water bridges: B:T.90, B:W.137 GOL.9: 8 residues within 4Å: Chain C: W.16, H.54, F.94, W.137, E.181, D.245, D.287 Ligands: MG.7 2 PLIP interactions: 2 interactions with chain C Water bridges: C:T.90, C:T.91 GOL.12: 8 residues within 4Å: Chain D: W.16, H.54, F.94, W.137, E.181, D.245, D.287 Ligands: MG.10 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.245 Water bridges: D:T.90, D:W.137

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
B

C
A

D
B

Xylose isomerase

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