Research workbench
Crystal structure of human thrombin mutant N143P in E:NA+ form
Analyse Crystal structure of human thrombin mutant N143P in E:NA+ form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3JZ1
- 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, NA, NO3
- Pockets
- 3 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 30 | 40% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 248 | 15% helix, 35% strand | P00734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- NA · Sodium ion · metal · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 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 | 186 | 0.50 | 0.77 | 30 | empty |
| 2 | 56 | 0.33 | 0.77 | 14 | GOL |
| 3 | 58 | 0.30 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1175 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3JZ1 · Crystal structure of human thrombin mutant N143P in E:Na+ form · 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 3JZ1 · PDBe 3JZ1 · UniProt P00734
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