Research workbench
Allosteric inhibition as a new mode of action for bay 1213790, a neutralizing antibody targeting the activated form of coagulation factor XI
Analyse Allosteric inhibition as a new mode of action for bay 1213790, a neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HHC
- Type
- protein
- Length
- 656 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fxia antibody Fab light chain; Fxia antibody Fab heavy chain; Coagulation factor XI
- EC
- 3.4.21.27
- UniProt
- P03951
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fxia antibody Fab light chain | protein | 213 | 6% helix, 50% strand | — |
| H | Fxia antibody Fab heavy chain | protein | 214 | 7% helix, 50% strand | — |
| A | Coagulation factor XI (EC 3.4.21.27) | protein | 229 | 12% helix, 34% strand | P03951 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.63 | 0.74 | 66 | SO4 |
| 2 | 295 | 0.59 | 0.78 | 34 | empty |
| 3 | 63 | 0.52 | 0.87 | 22 | empty |
| 4 | 94 | 0.36 | 0.75 | 28 | empty |
| 5 | 65 | 0.33 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1726 Ų buried · 9 hydrogen bonds · protein-protein
- H–A · 608 Ų buried · 11 hydrogen bonds · protein-protein
- L–A · 390 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6HHC · Allosteric Inhibition as a new mode of Action for BAY 1213790, a Neutralizing Antibody… · the same entry in another collection · chain L against L, TM-score 1.00
- P03951 · AlphaFold monomer V2.0 prediction for coagulation factor XI (P03951) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P03951
- Elsewhere: RCSB PDB 6HHC · PDBe 6HHC · UniProt P03951
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