MolNFT v1 · #5654 · protein
Design of P1' and P3' residues of trivalent thrombin inhibitors and their crystal structures
1EOJ · Alpha thrombin: “Design of P1' and P3' residues of trivalent thrombin inhibitors and their crystal structures”. X-ray diffraction, 1 ligand (BBS), 1 pocket (best druggability 0.28). MolNFT v1 #5654 on GenesisL1: 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
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