MolNFT v1 · #30501 · protein
Structure of thrombin in 400 mm potassium chloride
2A0Q · Thrombin, light chain: “Structure of thrombin in 400 mm potassium chloride”. X-ray diffraction, 3 ligands (NDG, K, CL), 4 pockets (best druggability 0.74). MolNFT v1 #30501 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2A0Q
- Type
- protein
- Length
- 545 residues
- Chains
- 4
- 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
- NDG, K, CL
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin, light chain | protein | 30 | 43% helix, 0% strand | P00734 |
| B | Thrombin, heavy chain (EC 3.4.21.5) | protein | 242 | 16% helix, 36% strand | P00734 |
| C | Thrombin, light chain | protein | 28 | 36% helix, 0% strand | P00734 |
| D | Thrombin, heavy chain (EC 3.4.21.5) | protein | 245 | 14% helix, 35% strand | P00734 |
Ligands and binding sites
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains B
- K · Potassium ion · metal · 2 copies · chains B, D
- CL · Chloride ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.74 | 0.78 | 84 | K |
| 2 | 402 | 0.63 | 0.78 | 61 | K, CL |
| 3 | 105 | 0.40 | 0.76 | 16 | empty |
| 4 | 66 | 0.27 | 0.72 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1192 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1097 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 612 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2A0Q · Structure of thrombin in 400 mM potassium chloride · 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 2A0Q · PDBe 2A0Q · UniProt P00734
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.