MolNFT v1 · #161882 · protein

X-ray radiation dose series on xylose isomerase - 2.63 mgy

6QRV: “X-ray radiation dose series on xylose isomerase - 2.63 mgy”. X-ray diffraction, 3 ligands (MN, MG, NA), 3 pockets (best druggability 0.73). MolNFT v1 #161882 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6QRV
Type: protein
Length: 387 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: MN, MG, NA
Pockets: 3 · best druggability 0.73

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Xylose isomerase (EC 5.3.1.5)	protein	387	50% helix, 11% strand	P24300

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains A
MG · Magnesium ion · metal · 2 copies · chains A
NA · Sodium ion · metal · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 12 copies · chains A
IPA · Isopropyl alcohol · additive · chains A

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

Pockets

3 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	58	0.73	0.98	23	EDO
2	545	0.66	0.77	50	EDO
3	66	0.46	0.83	13	empty

Compared structures

6QRV · X-ray radiation dose series on xylose isomerase - 2.63 MGy · 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 6QRV · PDBe 6QRV · UniProt P24300

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