Research workbench
Crystal structure determination of HUMAN/PORCINE chimera coagulation factor VIII
Analyse Crystal structure determination of HUMAN/PORCINE chimera 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
- 6MF0
- Type
- protein
- Length
- 2,503 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor VIII chimera
- UniProt
- P12263, P00451
- Ligands
- NAG, MAN, BMA, FUC, CA, ZN, CU1
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor VIII chimera | protein | 1256 | 6% helix, 38% strand | P12263, P00451 |
| B | Coagulation factor VIII chimera | protein | 1247 | 7% helix, 37% strand | P12263, P00451 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 11 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains B
- CA · Calcium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CU1 · Copper (I) 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.85 | 0.85 | 110 | empty |
| 2 | 500 | 0.84 | 0.90 | 53 | empty |
| 3 | 911 | 0.84 | 0.85 | 84 | empty |
| 4 | 1019 | 0.77 | 0.79 | 91 | NAG |
| 5 | 700 | 0.75 | 0.81 | 54 | empty |
Interfaces
1 interface between chains.
- A–B · 1334 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6MF0 · Crystal Structure Determination of Human/Porcine Chimera Coagulation Factor VIII · 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 0.99
- P00451 · AlphaFold monomer V2.0 prediction for coagulation factor VIII (P00451) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 6MF0 · PDBe 6MF0 · UniProt P12263 · UniProt P00451
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