MolNFT v1 · #38445 · protein
Design, synthesis, and characterization of a potent xylose isomerase inhibitor, D-threonohydroxamic acid, and high-resolution X-ray crystallographic structure of the enzyme-inhibitor complex
2GYI: “Design, synthesis, and characterization of a potent xylose isomerase inhibitor, D-threonohydroxamic acid, and…”. X-ray diffraction, 2 ligands (HYA, MG), 8 pockets (best druggability 0.82). MolNFT v1 #38445 on GenesisL1: 3D…
- PDB
- 2GYI
- Type
- protein
- Length
- 770 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xylose isomerase
- EC
- 5.3.1.5
- UniProt
- P15587
- Ligands
- HYA, MG
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Xylose isomerase (EC 5.3.1.5) | protein | 385 | 50% helix, 10% strand | P15587 |
Ligands and binding sites
- HYA · 2,3,4,N-tetrahydroxy-butyrimidic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.82 | 0.95 | 43 | empty |
| 2 | 849 | 0.79 | 0.82 | 88 | MG, HYA |
| 3 | 54 | 0.72 | 0.98 | 24 | empty |
| 4 | 95 | 0.49 | 0.82 | 14 | empty |
| 5 | 78 | 0.42 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1581 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 2GYI · Design, synthesis, and characterization of a potent xylose isomerase inhibitor… · the same entry in another collection · chain A against A, TM-score 1.00
- P15587 · AlphaFold monomer V2.0 prediction for xylose isomerase (P15587) · 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 P15587
- Elsewhere: RCSB PDB 2GYI · PDBe 2GYI · UniProt P15587
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.