SMTL ID : 6ybr.1

RT structure of Glucose Isomerase obtained at 1.20 A resolution from crystal grown in a Mylar microchip.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-tetramer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: E.217, H.220, 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.6 MG.2: 4 residues within 4Å: Chain A: E.181, E.217, D.245, D.287 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.3 MG.5: 4 residues within 4Å: Chain B: E.217, H.220, 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.18 MG.6: 4 residues within 4Å: Chain B: E.181, E.217, D.245, D.287 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.15 MG.9: 4 residues within 4Å: Chain C: E.217, H.220, 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.29 MG.10: 4 residues within 4Å: Chain C: E.181, E.217, D.245, D.287 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.23, H2O.26 MG.13: 4 residues within 4Å: Chain D: E.217, H.220, 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.40 MG.14: 4 residues within 4Å: Chain D: E.181, E.217, D.245, D.287 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.34, H2O.37

8 x NA: SODIUM ION(Non-functional Binders)

NA.3: 5 residues within 4Å: Chain A: D.163, L.206, E.207, R.208, Y.212 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.163, A:D.163, A:E.207, A:R.208 NA.4: 7 residues within 4Å: Chain A: V.218, Q.222, G.248, Q.249, A.262, G.263, D.264 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.222, A:Q.249, A:Q.249, A:D.264 NA.7: 5 residues within 4Å: Chain B: D.163, L.206, E.207, R.208, Y.212 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.163, B:E.207, B:R.208, B:Y.212 NA.8: 7 residues within 4Å: Chain B: V.218, Q.222, G.248, Q.249, A.262, G.263, D.264 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.222, B:Q.222, B:Q.249, B:D.264 NA.11: 5 residues within 4Å: Chain C: D.163, L.206, E.207, R.208, Y.212 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.207, C:R.208, C:Y.212, C:Y.212 NA.12: 7 residues within 4Å: Chain C: V.218, Q.222, G.248, Q.249, A.262, G.263, D.264 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:Q.222, C:Q.222, C:Q.249, C:D.264 NA.15: 5 residues within 4Å: Chain D: D.163, L.206, E.207, R.208, Y.212 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.207, D:R.208, D:Y.212, D:Y.212 NA.16: 7 residues within 4Å: Chain D: V.218, Q.222, G.248, Q.249, A.262, G.263, D.264 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.222, D:Q.249, D:A.262, D:D.264

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gavira, J.A. et al., Attaining atomic resolution from in situ data collection at room temperature using counter-diffusion-based low-cost microchips. Acta Crystallogr D Struct Biol (2020)

Release Date

2020-08-12

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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