MolNFT v1 · #38173 · protein
Crystal structure of the slow form of thrombin in a self-inhibited conformation
2GP9 · Prothrombin: “Crystal structure of the slow form of thrombin in a self-inhibited conformation”. X-ray diffraction, 4 pockets (best druggability 0.53). MolNFT v1 #38173 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2GP9
- Type
- protein
- Length
- 279 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 32 | 31% helix, 0% strand | P00734 |
| B | Prothrombin (EC 3.4.21.5) | protein | 247 | 16% helix, 34% strand | P00734 |
Ligands and binding sites
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.53 | 0.80 | 29 | empty |
| 2 | 73 | 0.43 | 0.81 | 24 | empty |
| 3 | 85 | 0.39 | 0.77 | 18 | empty |
| 4 | 57 | 0.27 | 0.73 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1259 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2GP9 · Crystal structure of the slow form of thrombin in a self-inhibited conformation · 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 2GP9 · PDBe 2GP9 · UniProt P00734
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.