Research workbench
Anophelin from the malaria vector inhibits thrombin through a novel reverse-binding mechanism
Analyse Anophelin from the malaria vector inhibits thrombin through a novel… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4E06
- Type
- protein
- Length
- 308 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Salivary anti-thrombin peptide anophelin
- EC
- 3.4.21.5
- UniProt
- P00734, Q9NJS1
- Ligands
- NAG, NA
- Pockets
- 3 · best druggability 0.33
Structure
x-ray diffraction · 3 distinct chains · 12% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin (EC 3.4.21.5) | protein | 28 | 32% helix, 0% strand | P00734 |
| H | Thrombin (EC 3.4.21.5) | protein | 252 | 10% helix, 35% strand | P00734 |
| I | Salivary anti-thrombin peptide anophelin | protein | 28 | 11% helix, 11% strand | Q9NJS1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.33 | 0.78 | 13 | empty |
| 2 | 58 | 0.28 | 0.74 | 17 | empty |
| 3 | 63 | 0.28 | 0.73 | 13 | empty |
Interfaces
2 interfaces between chains.
- H–I · 1473 Ų buried · 27 hydrogen bonds · protein-protein
- L–H · 1116 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4E06 · Anophelin from the malaria vector inhibits thrombin through a novel reverse-binding… · the same entry in another collection · chain L against L, 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 P00734
- Every structure of UniProt Q9NJS1
- Elsewhere: RCSB PDB 4E06 · PDBe 4E06 · UniProt P00734 · UniProt Q9NJS1
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