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Room-temperature joint X-RAY/NEUTRON structure of D-xylose isomerase in complex with 2NI2+ and per-deuterated D-sorbitol at pH 5.9

Analyse Room-temperature joint X-RAY/NEUTRON structure of D-xylose isomerase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4DVO
Type: protein
Length: 388 residues
Chains: 1
Method: neutron diffraction; x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xylose isomerase
EC: 5.3.1.5
UniProt: P24300
Ligands: SOR, NI
Pockets: 5 · best druggability 0.71

Structure

neutron diffraction; x-ray diffraction · 1 distinct chain · 49% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xylose isomerase (EC 5.3.1.5)	protein	388	49% helix, 11% strand	P24300

Ligands and binding sites

SOR · sorbitol · ligand · chains A
NI · Nickel (II) ion · metal · 3 copies · chains A

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

Pockets

5 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	51	0.71	0.99	25	empty
2	482	0.66	0.78	46	NI, SOR
3	98	0.50	0.82	14	empty
4	56	0.36	0.79	13	empty
5	60	0.27	0.73	14	empty

Compared structures

4DVO · Room-temperature joint X-ray/neutron structure of D-xylose isomerase in complex with… · the same entry in another collection · 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 4DVO · PDBe 4DVO · UniProt P24300

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