Research workbench
Crystal structure of a truncated B-domain human factor VIII
Analyse Crystal structure of a truncated B-domain human factor VIII in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BDV
- Type
- protein
- Length
- 1,218 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Factor viiia heavy chain, 92 kda isoform, B domain; Factor viiia light chain
- UniProt
- P00451
- Ligands
- NAG, BMA, ZN, CA, CU1
- Pockets
- 17 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Factor viiia heavy chain, 92 kda isoform, B domain | protein | 612 | 6% helix, 35% strand | P00451 |
| B | Factor viiia light chain | protein | 606 | 3% helix, 42% strand | P00451 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains B
- ZN · Zinc ion · metal · chains A
- CA · Calcium ion · metal · chains A
- CU1 · Copper (I) ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 608 | 0.87 | 0.91 | 55 | EDO |
| 2 | 1038 | 0.78 | 0.80 | 81 | NAG, EDO |
| 3 | 537 | 0.69 | 0.79 | 54 | empty |
| 4 | 279 | 0.65 | 0.81 | 42 | empty |
| 5 | 459 | 0.64 | 0.77 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 3673 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 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 4BDV · PDBe 4BDV · UniProt P00451
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