MolNFT v1 · #165462 · protein
Crystal structure of the catalytic domain of coagulation factor xia in complex with double bridged peptide F19
6TWB: “Crystal structure of the catalytic domain of coagulation factor xia in complex with double bridged peptide F19”. X-ray diffraction, 3 ligands (CSA, NH4, NH2), 2 pockets (best druggability 0.45). MolNFT v1 #165462 on GenesisL1: 3D…
- 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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