MolNFT v1 · #119070 · protein
Structure of a hydrolase bound with an inhibitor
5FKY · O-glcnacase BT_4395: “Structure of a hydrolase bound with an inhibitor”. X-ray diffraction, 1 ligand (2J4), 16 pockets (best druggability 0.62). MolNFT v1 #119070 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FKY
- Type
- protein
- Length
- 1,289 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- O-glcnacase BT_4395
- EC
- 3.2.1.169
- UniProt
- Q89ZI2
- Ligands
- 2J4
- Pockets
- 16 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-glcnacase BT_4395 (EC 3.2.1.169) | protein | 644 | 43% helix, 19% strand | Q89ZI2 |
| B | O-glcnacase BT_4395 (EC 3.2.1.169) | protein | 645 | 41% helix, 19% strand | Q89ZI2 |
Ligands and binding sites
- 2J4 · (3aR,5R,6S,7R,7aR)-2-amino-5-(hydroxymethyl)-5,6,7,7a-tetrahydro-3aH-pyrano[3,2-d][1,3]thiazole-6,7-diol · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.62 | 0.78 | 36 | empty |
| 2 | 287 | 0.59 | 0.78 | 37 | empty |
| 3 | 301 | 0.58 | 0.77 | 30 | empty |
| 4 | 84 | 0.57 | 0.86 | 19 | 2J4 |
| 5 | 97 | 0.54 | 0.84 | 20 | 2J4 |
Interfaces
1 interface between chains.
- A–B · 391 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 Q89ZI2
- Elsewhere: RCSB PDB 5FKY · PDBe 5FKY · UniProt Q89ZI2
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