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Human Coagulation Factor XIIa (FXIIa) bound with the macrocyclic peptide F3 containing two (1S,2S)-2-ACHC residues
Analyse Human Coagulation Factor XIIa (FXIIa) bound with the macrocyclic peptide F3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L63
- Type
- protein
- Length
- 493 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Coagulation factor XII; F3
- EC
- 3.4.21.38
- UniProt
- P00748
- Ligands
- ACE, NAG
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · resolution 3 · 3 distinct chains · 10% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor XII (EC 3.4.21.38) | protein | 228 | 10% helix, 36% strand | P00748 |
| B, D | F3 | protein | 18 | 0% helix, 11% strand | — |
| C | Coagulation factor XII (EC 3.4.21.38) | protein | 229 | 10% helix, 34% strand | P00748 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.53 | 0.79 | 25 | empty |
| 2 | 147 | 0.47 | 0.77 | 25 | empty |
Interfaces
3 interfaces between chains.
- C–D · 867 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 867 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 551 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 4 covalent, 4 d-amino, 4 modified, 2 glycan (disulfide, covalent ligand, D-amino acid, nonstandard, N-glycosylation).
Compared structures
- 6L63 · Human coagulation factor xiia (fxiia) bound with the macrocyclic peptide F3 containing… · 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 A against A, TM-score 0.97
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 6L63 · PDBe 6L63 · UniProt P00748
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