Research workbench
Design of P1' and P3' residues of trivalent thrombin inhibitors and their crystal structures
Analyse Design of P1' and P3' residues of trivalent thrombin inhibitors and their… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EOJ
- Type
- protein
- Length
- 291 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha thrombin; Thrombin inhibitor P798
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- BBS
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha thrombin (EC 3.4.21.5) | protein | 278 | 17% helix, 31% strand | P00734 |
| B | Thrombin inhibitor P798 | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- BBS · 4-tert-butylbenzenesulfonic acid · ligand · chains A, B
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 | 61 | 0.28 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1100 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 3 modified, 1 covalent (disulfide, nonstandard, covalent ligand).
Compared structures
- 1EOJ · Design of P1' and P3' residues of trivalent thrombin inhibitors and their crystal… · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 1EOJ · PDBe 1EOJ · UniProt P00734
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.