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Structure of glucose isomerase derivatized with kr.

Analyse Structure of glucose isomerase derivatized with kr. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1O1H
Type: protein
Length: 772 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xylose isomerase
EC: 5.3.1.5
UniProt: P24300
Ligands: CA, MG, CL, KR
Pockets: 7 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Xylose isomerase (EC 5.3.1.5)	protein	386	50% helix, 11% strand	P24300

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 4 copies · chains A, B
KR · Krypton · ion · 4 copies · chains A, B
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.72	0.99	23	KR
2	511	0.66	0.77	49	TRS, MPD
3	450	0.66	0.78	52	TRS, MPD
4	196	0.59	0.81	36	empty
5	211	0.58	0.80	36	empty

Interfaces

1 interface between chains.

A–B · 4828 Å² buried · 79 hydrogen bonds · protein-protein

Compared structures

1O1H · Structure of glucose isomerase derivatized with kr. · the same entry in another collection · chain A against A, TM-score 1.00
P24300 · AlphaFold monomer V2.0 prediction for xylose isomerase (P24300) · a predicted model of the same protein · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P24300
Elsewhere: RCSB PDB 1O1H · PDBe 1O1H · UniProt P24300

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