MolNFT v1 · #59974 · protein
Crystal structure of human factor VIII
3CDZ · Coagulation factor VIII heavy chain: “Crystal structure of human factor VIII”. X-ray diffraction, 4 ligands (NAG, MAN, CU), 20 pockets (best druggability 0.85). MolNFT v1 #59974 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3CDZ
- Type
- protein
- Length
- 1,261 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VIII heavy chain; Coagulation factor VIII light chain
- UniProt
- P00451
- Ligands
- NAG, MAN, CU, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor VIII heavy chain | protein | 630 | 7% helix, 25% strand | P00451 |
| B | Coagulation factor VIII light chain | protein | 631 | 3% helix, 38% strand | P00451 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains B
- CU · Copper (II) ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 479 | 0.85 | 0.92 | 56 | empty |
| 2 | 162 | 0.78 | 0.94 | 41 | empty |
| 3 | 662 | 0.75 | 0.81 | 74 | empty |
| 4 | 57 | 0.74 | 0.99 | 17 | empty |
| 5 | 66 | 0.73 | 0.97 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3676 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 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 3CDZ · PDBe 3CDZ · UniProt P00451
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