MolNFT v1 · #2611 · protein
Recruiting zinc to mediate potent, specific inhibition of serine proteases
1C1V · Thrombin light chain: “Recruiting zinc to mediate potent, specific inhibition of serine proteases”. X-ray diffraction, 3 ligands (BAB, ZN, NA), 2 pockets (best druggability 0.53). MolNFT v1 #2611 on GenesisL1: 3D structure, binding…
- PDB
- 1C1V
- Type
- protein
- Length
- 299 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Hirudin-2
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- BAB, ZN, NA
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 36 | 28% helix, 8% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 252 | 15% helix, 34% strand | P00734 |
| I | Hirudin-2 | protein | 11 | 27% helix, 0% strand | P28504 |
Ligands and binding sites
- BAB · Bis(5-amidino-benzimidazolyl)methane · ligand · chains H
- ZN · Zinc ion · metal · 2 copies · chains H
- NA · Sodium ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.53 | 0.76 | 41 | ZN, BAB |
| 2 | 59 | 0.30 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1402 Ų buried · 25 hydrogen bonds · protein-protein
- H–I · 676 Ų buried · 9 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 1C1V · PDBe 1C1V · UniProt P00734 · UniProt P28504
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