MolNFT v1 · #234 · protein

Xylose isomerase from bacillus stearothermophilus

1A0D: “Xylose isomerase from bacillus stearothermophilus”. X-ray diffraction, 1 ligand (MN), 20 pockets (best druggability 0.88). MolNFT v1 #234 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1A0D
Type: protein
Length: 1,748 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Xylose isomerase
EC: 5.3.1.5
UniProt: P54273
Ligands: MN
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Xylose isomerase (EC 5.3.1.5)	protein	437	49% helix, 12% strand	P54273

Ligands and binding sites

MN · Manganese (II) ion · metal · 8 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	637	0.88	0.93	107	empty
2	597	0.87	0.93	94	empty
3	698	0.85	0.89	46	empty
4	150	0.78	0.95	38	empty
5	95	0.76	0.97	23	empty

Interfaces

6 interfaces between chains.

C–D · 4138 Å² buried · 44 hydrogen bonds · protein-protein
A–B · 4124 Å² buried · 43 hydrogen bonds · protein-protein
A–D · 1958 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 1946 Å² buried · 28 hydrogen bonds · protein-protein
B–D · 1371 Å² buried · 20 hydrogen bonds · protein-protein

Compared structures

1A0D · Xylose isomerase from bacillus stearothermophilus · the same entry in another collection · chain C against C, TM-score 1.00
P54273 · AlphaFold monomer V2.0 prediction for xylose isomerase (P54273) · 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 P54273
Elsewhere: RCSB PDB 1A0D · PDBe 1A0D · UniProt P54273

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.