MolNFT v1 · #23330 · protein
Crystal structure of the thrombin mutant D221A/D222K
1TWX · Prothrombin: “Crystal structure of the thrombin mutant D221A/D222K”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.57). MolNFT v1 #23330 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1TWX
- Type
- protein
- Length
- 290 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; Hirudin
- EC
- 3.4.21.5
- UniProt
- P00734, P28504
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 28 | 32% helix, 0% strand | P00734 |
| B | Prothrombin (EC 3.4.21.5) | protein | 252 | 13% helix, 35% strand | P00734 |
| C | Hirudin | protein | 10 | 0% helix, 0% strand | P28504 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 314 | 0.57 | 0.76 | 42 | empty |
| 2 | 65 | 0.33 | 0.76 | 20 | empty |
| 3 | 63 | 0.28 | 0.73 | 13 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1080 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 646 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan, 1 modified (disulfide, N-glycosylation, sulfation).
Compared structures
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
- Every structure of UniProt P28504
- Elsewhere: RCSB PDB 1TWX · PDBe 1TWX · UniProt P00734 · UniProt P28504
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.