MolNFT v1 · #30035 · protein
Thrombin in complex with an azafluorenyl inhibitor 23B
1ZRB: “Thrombin in complex with an azafluorenyl inhibitor 23B”. X-ray diffraction, 1 ligand (062), 1 pocket (best druggability 0.56). MolNFT v1 #30035 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1ZRB
- Type
- protein
- Length
- 286 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; 11-peptide hirudin fragment
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- 062
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin (EC 3.4.21.5) | protein | 276 | 17% helix, 32% strand | P00734 |
| B | 11-peptide hirudin fragment | protein | 10 | 0% helix, 0% strand | P28504 |
Ligands and binding sites
- 062 · 3-aza-9-hydroxy-9-fluorenylcarbonyl-L-prolyl-2-aminomethyl-5-chlorobenzylamide, N-oxide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 238 | 0.56 | 0.78 | 38 | 062 |
Interfaces
1 interface between chains.
- A–B · 669 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 modified (disulfide, sulfation).
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 P00734
- Every structure of UniProt P28504
- Elsewhere: RCSB PDB 1ZRB · PDBe 1ZRB · UniProt P00734 · UniProt P28504
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.