MolNFT v1 · #111108 · protein
Reversal agent for dabigatran
4YGV · Adabi-FAB2A heavy chain: “Reversal agent for dabigatran”. X-ray diffraction, 12 pockets (best druggability 0.64). MolNFT v1 #111108 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4YGV
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adabi-FAB2A heavy chain; Adabi-FAB2A light chain
- Pockets
- 12 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Adabi-FAB2A heavy chain | protein | 220 | 10% helix, 50% strand | — |
| B, L | Adabi-FAB2A light chain | protein | 218 | 6% helix, 50% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains A, B, F, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.64 | 0.74 | 58 | empty |
| 2 | 302 | 0.61 | 0.79 | 42 | empty |
| 3 | 535 | 0.61 | 0.74 | 59 | empty |
| 4 | 53 | 0.55 | 0.90 | 22 | GOL |
| 5 | 140 | 0.54 | 0.81 | 26 | empty |
Interfaces
4 interfaces between chains.
- F–L · 1936 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1919 Ų buried · 18 hydrogen bonds · protein-protein
- A–F · 341 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 147 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4YGV · Reversal Agent for Dabigatran · the same entry in another collection · 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
- Elsewhere: RCSB PDB 4YGV · PDBe 4YGV
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.