Research workbench
Crystal structure of human prothrombin mutant S101C/A470C
Analyse Crystal structure of human prothrombin mutant S101C/A470C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6C2W
- Type
- protein
- Length
- 1,150 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, BMA, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 14% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Prothrombin (EC 3.4.21.5) | protein | 575 | 14% helix, 14% strand | P00734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MG · Magnesium ion · metal · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.79 | 0.96 | 28 | empty |
| 2 | 983 | 0.79 | 0.81 | 125 | empty |
| 3 | 244 | 0.78 | 0.91 | 40 | empty |
| 4 | 522 | 0.77 | 0.84 | 60 | empty |
| 5 | 765 | 0.74 | 0.79 | 81 | empty |
Interfaces
1 interface between chains.
- A–B · 744 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 20 modified, 4 glycan (disulfide, carboxylation, N-glycosylation).
Compared structures
- 6C2W · Crystal structure of human prothrombin mutant S101C/A470C · 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 6C2W · PDBe 6C2W · UniProt P00734
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