Research workbench
Crystal structure of insect derived double domain kazal inhibitor rhodniin in complex with thrombin
Analyse Crystal structure of insect derived double domain kazal inhibitor rhodniin in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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