Research workbench
Crystal structure of Ca2+ bound prothrombin deletion mutant residues 146-167
Analyse Crystal structure of Ca2+ bound prothrombin deletion mutant residues 146-167 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4O03
- Type
- protein
- Length
- 539 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.38
- Source
- Homo sapiens
- Molecule
- Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NAG, CA
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · resolution 3.38 · 1 distinct chain · 13% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 539 | 13% helix, 19% strand | P00734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.69 | 0.77 | 65 | empty |
| 2 | 122 | 0.56 | 0.83 | 23 | empty |
| 3 | 165 | 0.52 | 0.79 | 28 | empty |
| 4 | 89 | 0.49 | 0.82 | 19 | empty |
| 5 | 156 | 0.47 | 0.77 | 23 | empty |
Modifications
Observed in the structure: 12 disulfide, 10 modified, 3 glycan (disulfide, carboxylation, N-glycosylation).
Compared structures
- 4O03 · Crystal structure of CA2+ bound prothrombin deletion mutant residues 146-167 · 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 4O03 · PDBe 4O03 · UniProt P00734
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