MolNFT v1 · #119073 · protein
Structure of a hydrolase with an inhibitor
5FL1 · O-glcnacase BT_4395: “Structure of a hydrolase with an inhibitor”. X-ray diffraction, 2 ligands (DV1, CA), 20 pockets (best druggability 0.68). MolNFT v1 #119073 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FL1
- Type
- protein
- Length
- 1,368 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
- DV1, CA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-glcnacase BT_4395 (EC 3.2.1.169) | protein | 703 | 39% helix, 20% strand | Q89ZI2 |
| B | O-glcnacase BT_4395 (EC 3.2.1.169) | protein | 665 | 40% helix, 19% strand | Q89ZI2 |
Ligands and binding sites
- DV1 · (3~{a}~{R},5~{R},6~{S},7~{R},7~{a}~{R})-5-(hydroxymethyl)-2-(prop-2-enylamino)-5,6,7,7~{a}-tetrahydro-3~{a}~{H}-pyrano[3,2-d][1,3]thiazole-6,7-diol · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.68 | 0.78 | 67 | empty |
| 2 | 449 | 0.66 | 0.78 | 40 | empty |
| 3 | 428 | 0.63 | 0.77 | 47 | empty |
| 4 | 98 | 0.61 | 0.87 | 22 | DV1 |
| 5 | 99 | 0.59 | 0.86 | 24 | DV1, EDO |
Interfaces
1 interface between chains.
- A–B · 1135 Ų buried · 24 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 5FL1 · PDBe 5FL1 · UniProt Q89ZI2
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