Research workbench
Structure of GH84 with ligand
Analyse Structure of GH84 with ligand in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ABG
- Type
- protein
- Length
- 1,325 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, 3.2.1.52
- UniProt
- Q89ZI2
- Ligands
- V0N, CA
- Pockets
- 17 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | O-glcnacase BT_4395 (EC 3.2.1.169, 3.2.1.52) | protein | 663 | 41% helix, 19% strand | Q89ZI2 |
| B | O-glcnacase BT_4395 (EC 3.2.1.169, 3.2.1.52) | protein | 662 | 39% helix, 19% strand | Q89ZI2 |
Ligands and binding sites
- V0N · 2-[(2R,3S,4R,5R)-1-[3-(4-fluorophenyl)propyl]-5-(hydroxymethyl)-3,4-bis(oxidanyl)pyrrolidin-2-yl]-N-methyl-ethanamide · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 491 | 0.67 | 0.78 | 49 | empty |
| 2 | 456 | 0.65 | 0.78 | 60 | empty |
| 3 | 428 | 0.62 | 0.77 | 46 | empty |
| 4 | 97 | 0.56 | 0.85 | 19 | V0N |
| 5 | 98 | 0.56 | 0.85 | 20 | V0N |
Interfaces
1 interface between chains.
- A–B · 1084 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- Q89ZI2 · AlphaFold monomer V2.0 prediction for O-glcnacase BT_4395 (Q89ZI2) · 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 Q89ZI2
- Elsewhere: RCSB PDB 5ABG · PDBe 5ABG · UniProt Q89ZI2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.