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Crystal structure of the Vitronectin hemopexin-like domain
Analyse Crystal structure of the Vitronectin hemopexin-like domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O5E
- Type
- protein
- Length
- 366 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.9
- Source
- Homo sapiens
- Molecule
- Vitronectin
- UniProt
- P04004
- Ligands
- NA, SO4, CL, NO3
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · resolution 1.9 · 2 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitronectin | protein | 189 | 10% helix, 40% strand | P04004 |
| B | Vitronectin | protein | 177 | 9% helix, 43% strand | P04004 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · chains A, B
- IMD · Imidazole · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.76 | 0.85 | 63 | IMD, NO3 |
| 2 | 97 | 0.45 | 0.79 | 21 | empty |
| 3 | 95 | 0.40 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 940 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
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 P04004
- Elsewhere: RCSB PDB 6O5E · PDBe 6O5E · UniProt P04004
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