Research workbench
Crystal structure of the C1QTNF5 globular domain in space group P63
Analyse Crystal structure of the C1QTNF5 globular domain in space group P63 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NN0
- Type
- protein
- Length
- 416 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.42
- Source
- Homo sapiens
- Molecule
- Complement C1q tumor necrosis factor-related protein 5
- UniProt
- Q9BXJ0
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · resolution 1.42 · 3 distinct chains · 0% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement C1q tumor necrosis factor-related protein 5 | protein | 137 | 0% helix, 55% strand | Q9BXJ0 |
| B | Complement C1q tumor necrosis factor-related protein 5 | protein | 141 | 0% helix, 53% strand | Q9BXJ0 |
| C | Complement C1q tumor necrosis factor-related protein 5 | protein | 138 | 0% helix, 53% strand | Q9BXJ0 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B, C
- ACT · Acetate ion · additive · 2 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.58 | 0.89 | 19 | ACT |
| 2 | 72 | 0.58 | 0.89 | 19 | EDO, ACT |
| 3 | 219 | 0.55 | 0.78 | 29 | EDO |
Interfaces
2 interfaces between chains.
- A–B · 807 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 488 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4NN0 · Crystal structure of the C1QTNF5 globular domain in space group P63 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BXJ0 · AlphaFold monomer V2.0 prediction for complement C1Q tumor necrosis factor-related… · 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 Q9BXJ0
- Elsewhere: RCSB PDB 4NN0 · PDBe 4NN0 · UniProt Q9BXJ0
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