MolNFT v1 · #121667 · protein
Human recombinant coagulation fxi in complex with a peptide derived from human high molecular weight kininogen (hkp)
5I25 · Coagulation factor XI: “Human recombinant coagulation fxi in complex with a peptide derived from human high molecular weight…”. X-ray diffraction, 1 ligand (NAG), 9 pockets (best druggability 0.81). MolNFT v1 #121667 on GenesisL1…
- PDB
- 5I25
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor XI; Asn-pro-ile-ser-asp-phe-pro-asp
- EC
- 3.4.21.27
- UniProt
- P03951
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Coagulation factor XI (EC 3.4.21.27) | protein | 596 | 16% helix, 35% strand | P03951 |
| B | Asn-pro-ile-ser-asp-phe-pro-asp | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.81 | 0.86 | 64 | empty |
| 2 | 394 | 0.67 | 0.80 | 35 | empty |
| 3 | 290 | 0.63 | 0.80 | 39 | empty |
| 4 | 79 | 0.60 | 0.89 | 22 | empty |
| 5 | 90 | 0.41 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 507 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5I25 · human recombinant coagulation FXI in complex with a peptide derived from human high… · 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 0.68
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 5I25 · PDBe 5I25 · UniProt P03951
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