MolNFT v1 · #160903 · protein
Crystal structure of human thrombin mutant D194A
6PXQ · Thrombin light chain: “Crystal structure of human thrombin mutant D194A”. X-ray diffraction, 1 ligand (NAG), 3 pockets (best druggability 0.46). MolNFT v1 #160903 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6PXQ
- Type
- protein
- Length
- 278 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 33 | 12% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 245 | 12% helix, 35% strand | P00734 |
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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.46 | 0.78 | 18 | empty |
| 2 | 122 | 0.46 | 0.78 | 23 | empty |
| 3 | 56 | 0.26 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1223 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6PXQ · Crystal structure of human thrombin mutant D194A · 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 6PXQ · PDBe 6PXQ · UniProt P00734
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