Research workbench
Crystal structure of the human factor VIII C2 domain in complex with murine 3E6 inhibitory antibody
Analyse Crystal structure of the human factor VIII C2 domain in complex with murine 3E6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XZU
- Type
- protein
- Length
- 1,137 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3E6 antibody Fab heavy chain; 3E6 antibody Fab light chain; Coagulation factor VIII
- UniProt
- P00451
- Ligands
- MG
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3E6 antibody Fab heavy chain | protein | 213 | 6% helix, 52% strand | — |
| B | 3E6 antibody Fab light chain | protein | 213 | 5% helix, 52% strand | — |
| M, G | Coagulation factor VIII | protein | 154 | 4% helix, 53% strand | P00451 |
| E | 3E6 antibody Fab heavy chain | protein | 208 | 7% helix, 51% strand | — |
| F | 3E6 antibody Fab light chain | protein | 195 | 7% helix, 46% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, M, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.79 | 0.84 | 71 | empty |
| 2 | 170 | 0.71 | 0.90 | 34 | empty |
| 3 | 441 | 0.59 | 0.75 | 55 | empty |
| 4 | 378 | 0.59 | 0.76 | 44 | empty |
| 5 | 336 | 0.55 | 0.75 | 51 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1885 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1655 Ų buried · 18 hydrogen bonds · protein-protein
- B–G · 424 Ų buried · 3 hydrogen bonds · protein-protein
- E–G · 423 Ų buried · 14 hydrogen bonds · protein-protein
- A–M · 420 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 4XZU · Crystal Structure of the Human Factor VIII C2 Domain in Complex with Murine 3E6… · the same entry in another collection · chain G against G, TM-score 1.00
- P00451 · AlphaFold monomer V2.0 prediction for coagulation factor VIII (P00451) · a predicted model of the same protein · chain M 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 P00451
- Elsewhere: RCSB PDB 4XZU · PDBe 4XZU · UniProt P00451
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