Research workbench
Structure of recombinant gla-domainless prothrombin mutant S525A
Analyse Structure of recombinant gla-domainless prothrombin mutant S525A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HZH
- Type
- protein
- Length
- 860 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 392 | 14% helix, 23% strand | P00734 |
| B | Prothrombin (EC 3.4.21.5) | protein | 468 | 8% helix, 22% strand | P00734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.60 | 0.78 | 47 | empty |
| 2 | 336 | 0.58 | 0.77 | 33 | empty |
| 3 | 250 | 0.53 | 0.76 | 30 | empty |
| 4 | 214 | 0.51 | 0.76 | 28 | empty |
| 5 | 177 | 0.50 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 162 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4HZH · Structure of recombinant Gla-domainless prothrombin mutant S525A · 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 4HZH · PDBe 4HZH · UniProt P00734
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