Research workbench
Factor VIII in complex with the anti-C2 domain antibody, G99
Analyse Factor VIII in complex with the anti-C2 domain antibody, G99 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KBT
- Type
- protein
- Length
- 1,444 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, CU, ZN, CA
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor VIII,COAGULATION factor VIII,COAGULATION factor VIII,COAGULATION factor VIII,COAGULATION factor VIII | protein | 1233 | 6% helix, 38% strand | P12263, P00451 |
| E | G99 heavy chain | protein | 115 | 3% helix, 26% strand | — |
| F | G99 light chain | protein | 96 | 0% helix, 27% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- CU · Copper (II) ion · metal · chains A
- ZN · Zinc ion · metal · chains A
- 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.83 | 0.88 | 64 | empty |
| 2 | 260 | 0.83 | 0.95 | 31 | empty |
| 3 | 125 | 0.78 | 0.95 | 38 | empty |
| 4 | 1108 | 0.76 | 0.78 | 85 | NAG |
| 5 | 295 | 0.74 | 0.86 | 58 | empty |
Interfaces
3 interfaces between chains.
- A–E · 671 Ų buried · 4 hydrogen bonds · protein-protein
- E–F · 561 Ų buried · 5 hydrogen bonds · protein-protein
- A–F · 269 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 7KBT · Factor VIII in complex with the anti-C2 domain antibody, G99 · the same entry in another collection · chain A against A, TM-score 1.00
- P12263 · AlphaFold monomer V2.0 prediction for coagulation factor VIII (P12263) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P00451 · AlphaFold monomer V2.0 prediction for coagulation factor VIII (P00451) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 7KBT · PDBe 7KBT · UniProt P12263 · UniProt P00451
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