Research workbench
Structures of the two-chain human plasma factor xiia co-crystallized with potent inhibitors
Analyse Structures of the two-chain human plasma factor xiia co-crystallized with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6B77
- Type
- protein
- Length
- 252 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor XII
- EC
- 3.4.21.38
- UniProt
- P00748
- Ligands
- CWV, NAG, SO4, IOD
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor XII (EC 3.4.21.38) | protein | 9 | 0% helix, 11% strand | P00748 |
| B | Coagulation factor XII (EC 3.4.21.38) | protein | 243 | 11% helix, 35% strand | P00748 |
Ligands and binding sites
- CWV · [3-(1-aminoisoquinolin-6-yl)phenyl]boronic acid · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B
- SO4 · Sulfate ion · ion · 3 copies · chains B
- IOD · Iodide ion · ion · 2 copies · chains B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 109 | 0.52 | 0.82 | 24 | empty |
| 2 | 139 | 0.46 | 0.77 | 35 | CWV, SO4 |
| 3 | 96 | 0.36 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 372 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 6B77 · Structures of the two-chain human plasma factor XIIa co-crystallized with potent… · the same entry in another collection · chain A against A, TM-score 1.00
- P00748 · AlphaFold monomer V2.0 prediction for coagulation factor XII (P00748) · a predicted model of the same protein · chain B 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 P00748
- Elsewhere: RCSB PDB 6B77 · PDBe 6B77 · UniProt P00748
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