MolNFT v1 · #22649 · protein
Crystal structure of insect derived double domain kazal inhibitor rhodniin in complex with thrombin
1TBQ: “Crystal structure of insect derived double domain kazal inhibitor rhodniin in complex with thrombin”. X-ray diffraction, 12 pockets (best druggability 0.62). MolNFT v1 #22649 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1TBQ
- Type
- protein
- Length
- 822 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Rhodniin
- EC
- 3.4.21.5
- UniProt
- P00735, Q06684
- Pockets
- 12 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, J | Thrombin (EC 3.4.21.5) | protein | 49 | 39% helix, 2% strand | P00735 |
| H, K | Thrombin (EC 3.4.21.5) | protein | 259 | 14% helix, 35% strand | P00735 |
| R, S | Rhodniin | protein | 103 | 15% helix, 20% strand | Q06684 |
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.62 | 0.80 | 34 | empty |
| 2 | 180 | 0.58 | 0.81 | 23 | empty |
| 3 | 108 | 0.55 | 0.84 | 21 | empty |
| 4 | 72 | 0.51 | 0.85 | 21 | empty |
| 5 | 145 | 0.49 | 0.79 | 20 | empty |
Interfaces
4 interfaces between chains.
- L–H · 1909 Ų buried · 32 hydrogen bonds · protein-protein
- H–R · 1875 Ų buried · 28 hydrogen bonds · protein-protein
- K–S · 1854 Ų buried · 27 hydrogen bonds · protein-protein
- J–K · 1788 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 1TBQ · Crystal structure of insect derived double domain kazal inhibitor rhodniin in complex… · the same entry in another collection · chain S against S, TM-score 1.00
- P00735 · AlphaFold monomer V2.0 prediction for prothrombin (P00735) · a predicted model of the same protein · chain H against A, TM-score 0.97
- Q06684 · AlphaFold monomer V2.0 prediction for thrombin inhibitor rhodniin (Q06684) · a predicted model of the same protein · chain R against A, TM-score 0.57
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 P00735
- Every structure of UniProt Q06684
- Elsewhere: RCSB PDB 1TBQ · PDBe 1TBQ · UniProt P00735 · UniProt Q06684
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