MolNFT v1 · #165121 · protein
Tsetse thrombin inhibitor in complex with human alpha-thrombin - orthorhombic form at 12KEV
6TKG · Prothrombin: “Tsetse thrombin inhibitor in complex with human alpha-thrombin - orthorhombic form at 12KEV”. X-ray diffraction, 2 ligands (NAG, NA), 1 pocket (best druggability 0.43). MolNFT v1 #165121 on GenesisL1: 3D structure…
- PDB
- 6TKG
- Type
- protein
- Length
- 313 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Tsetse thrombin inhibitor
- EC
- 3.4.21.5
- UniProt
- P00734, O97373
- Ligands
- NAG, NA
- Pockets
- 1 · best druggability 0.43
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Prothrombin (EC 3.4.21.5) | protein | 36 | 28% helix, 0% strand | P00734 |
| H | Prothrombin (EC 3.4.21.5) | protein | 252 | 16% helix, 35% strand | P00734 |
| I | Tsetse thrombin inhibitor | protein | 25 | 12% helix, 8% strand | O97373 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- NA · Sodium ion · metal · chains H
- GOL · Glycerol · additive · chains L, 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.43 | 0.78 | 24 | empty |
Interfaces
3 interfaces between chains.
- H–I · 1632 Ų buried · 33 hydrogen bonds · protein-protein
- L–H · 1438 Ų buried · 33 hydrogen bonds · protein-protein
- L–I · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 modified, 1 glycan (disulfide, sulfation, N-glycosylation).
Compared structures
- 6TKG · Tsetse thrombin inhibitor in complex with human alpha-thrombin - orthorhombic form at… · the same entry in another collection · chain L against L, TM-score 1.00
- O97373 · AlphaFold monomer V2.0 prediction for tsetse thrombin inhibitor (O97373) · a predicted model of the same protein · chain I against A, TM-score 0.17
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 O97373
- Elsewhere: RCSB PDB 6TKG · PDBe 6TKG · UniProt P00734 · UniProt O97373
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