MolNFT v1 · #16551 · protein
Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors
1O2G · Thrombin: “Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease…”. X-ray diffraction, 2 ligands (696, NA), 1 pocket (best druggability 0.56). MolNFT v1 #16551 on GenesisL1: 3D…
- PDB
- 1O2G
- Type
- protein
- Length
- 298 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Acetyl hirudin
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- 696, NA
- Pockets
- 1 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin (EC 3.4.21.5) | protein | 36 | 28% helix, 6% strand | P00734 |
| H | Thrombin (EC 3.4.21.5) | protein | 251 | 16% helix, 35% strand | P00734 |
| I | Acetyl hirudin | protein | 11 | 27% helix, 0% strand | P28504 |
Ligands and binding sites
- 696 · 3-{5-[amino(iminio)methyl]-1H-indol-2-yl}-1,1'-biphenyl-2-olate · ligand · chains H
- NA · Sodium ion · metal · chains H
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 | 300 | 0.56 | 0.76 | 42 | 696 |
Interfaces
2 interfaces between chains.
- L–H · 1433 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 662 Ų buried · 5 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 1O2G · PDBe 1O2G · UniProt P00734 · UniProt P28504
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