Research workbench
Crystal structure of HFA9 EGF repeat with O-glucose trisaccharide
Analyse Crystal structure of HFA9 EGF repeat with O-glucose trisaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VYG
- Type
- protein
- Length
- 128 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coagulation factor IX
- EC
- 3.4.21.22
- UniProt
- P00740
- Ligands
- XYS, BGC, CA
- Pockets
- 1 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Coagulation factor IX (EC 3.4.21.22) | protein | 43 | 0% helix, 26% strand | P00740 |
| C | Coagulation factor IX (EC 3.4.21.22) | protein | 42 | 0% helix, 29% strand | P00740 |
Ligands and binding sites
- XYS · alpha-D-xylopyranose · sugar · 6 copies · chains B, A, C
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains B, A, C
- CA · Calcium ion · metal · 3 copies · chains B, C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.37 | 0.75 | 23 | empty |
Interfaces
2 interfaces between chains.
- B–A · 439 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 424 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 3 glycan (disulfide, O-glycosylation).
Compared structures
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 P00740
- Elsewhere: RCSB PDB 5VYG · PDBe 5VYG · UniProt P00740
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