Research workbench
Crystal structure of the catalytic domain of coagulation factor xia in complex with double bridged peptide F19
Analyse Crystal structure of the catalytic domain of coagulation factor xia in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TWB
- Type
- protein
- Length
- 255 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor XI; Double bridged peptide F19
- EC
- 3.4.21.27
- UniProt
- P03951
- Ligands
- CSA, NH4, NH2
- Pockets
- 2 · best druggability 0.45
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor XI (EC 3.4.21.27) | protein | 238 | 13% helix, 35% strand | P03951 |
| H | Coagulation factor XI (EC 3.4.21.27) | protein | 8 | 0% helix, 0% strand | P03951 |
| B | Double bridged peptide F19 | protein | 9 | 0% helix, 11% strand | — |
Ligands and binding sites
- CSA · S-acetonylcysteine · ligand · chains A, B
- NH4 · Ammonium ion · ion · 3 copies · chains A, B
- NH2 · Amino group · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.45 | 0.79 | 17 | empty |
| 2 | 86 | 0.41 | 0.78 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 633 Ų buried · 16 hydrogen bonds · protein-protein
- A–H · 451 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 covalent, 1 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 6TWB · Crystal Structure of the Catalytic Domain of Coagulation Factor XIa in Complex with… · the same entry in another collection · chain A against A, 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 0.98
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 6TWB · PDBe 6TWB · UniProt P03951
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