Research workbench
Crystal structure analysis of coagulation factor VIII
Analyse Crystal structure analysis of coagulation factor VIII in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2R7E
- Type
- protein
- Length
- 1,337 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VIII
- UniProt
- P00451
- Ligands
- NAG, MAN, BMA, CA, CU
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor VIII | protein | 693 | 5% helix, 18% strand | P00451 |
| B | Coagulation factor VIII | protein | 644 | 2% helix, 23% strand | P00451 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B
- BMA · beta-D-mannopyranose · sugar · 3 copies
- CA · Calcium ion · metal · 3 copies · chains A
- CU · Copper (II) ion · metal · 2 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 | 771 | 0.85 | 0.87 | 86 | empty |
| 2 | 901 | 0.78 | 0.81 | 87 | empty |
| 3 | 354 | 0.76 | 0.87 | 54 | empty |
| 4 | 938 | 0.74 | 0.77 | 76 | empty |
| 5 | 544 | 0.72 | 0.80 | 58 | CA |
Interfaces
1 interface between chains.
- A–B · 3453 Ų buried · 31 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
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 P00451
- Elsewhere: RCSB PDB 2R7E · PDBe 2R7E · UniProt P00451
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