MolNFT v1 · #76903 · protein

Room temperature X-ray structure of D-xylose isomerase in complex with 0.6NI2+ cation bound in M2 metal binding site at PH=5.8

3QYS: “Room temperature X-ray structure of D-xylose isomerase in complex with 0.6NI2+ cation bound in M2 metal…”. X-ray diffraction, 1 ligand (NI), 4 pockets (best druggability 0.73). MolNFT v1 #76903 on GenesisL1: 3D structure, binding…

PDB: 3QYS
Type: protein
Length: 388 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xylose isomerase
EC: 5.3.1.5
UniProt: P24300
Ligands: NI
Pockets: 4 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xylose isomerase (EC 5.3.1.5)	protein	388	50% helix, 10% strand	P24300

Ligands and binding sites

NI · Nickel (II) ion · metal · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	60	0.73	0.98	22	empty
2	460	0.65	0.77	48	empty
3	95	0.50	0.82	14	empty
4	63	0.36	0.78	14	empty

Compared structures

3QYS · Room Temperature X-ray Structure of D-Xylose Isomerase in complex with 0.6Ni2+ cation… · 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 3QYS · PDBe 3QYS · UniProt P24300

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