Research workbench
Structure of blood coagulation factor VIII in complex with an anti-C1 domain pathogenic antibody inhibitor
Analyse Structure of blood coagulation factor VIII in complex with an anti-C1 domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7K66
- Type
- protein
- Length
- 1,695 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VIII,COAGULATION factor VIII,COAGULATION factor VIII,COAGULATION…
- UniProt
- P12263, P00451
- Ligands
- NAG, MAN, BMA, CU, CA, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor VIII,COAGULATION factor VIII,COAGULATION factor VIII,COAGULATION factor VIII | protein | 1265 | 6% helix, 36% strand | P12263, P00451 |
| B | 2A9 heavy chain | protein | 217 | 0% helix, 24% strand | — |
| C | 2A9 light chain | protein | 213 | 0% helix, 37% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- CU · Copper (II) ion · metal · chains A
- CA · Calcium ion · metal · chains A
- ZN · Zinc 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 386 | 0.86 | 0.94 | 55 | empty |
| 2 | 1159 | 0.78 | 0.79 | 107 | empty |
| 3 | 950 | 0.74 | 0.78 | 104 | empty |
| 4 | 58 | 0.74 | 0.99 | 19 | empty |
| 5 | 53 | 0.73 | 0.99 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1892 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 698 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 483 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7K66 · Structure of Blood Coagulation Factor VIII in Complex with an Anti-C1 Domain Pathogenic… · the same entry in another collection · chain A against A, TM-score 1.00
- P00451 · AlphaFold monomer V2.0 prediction for coagulation factor VIII (P00451) · a predicted model of the same protein · chain A against A, TM-score 0.95
- P12263 · AlphaFold monomer V2.0 prediction for coagulation factor VIII (P12263) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P12263
- Every structure of UniProt P00451
- Elsewhere: RCSB PDB 7K66 · PDBe 7K66 · UniProt P12263 · UniProt P00451
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