Research workbench
Crystal structure of gallus gallus beta-parvalbumin (avian thymic hormone)
Analyse Crystal structure of gallus gallus beta-parvalbumin (avian thymic hormone) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FS7
- Type
- protein
- Length
- 861 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Parvalbumin, thymic
- UniProt
- P19753
- Ligands
- CA, SO4
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, H | Parvalbumin, thymic | protein | 108 | 55% helix, 2% strand | P19753 |
| B, F, G | Parvalbumin, thymic | protein | 107 | 59% helix, 7% strand | P19753 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains A, B, C, D, E, F, G, H
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, G, H
- GOL · Glycerol · additive · 3 copies · chains C, D, H, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 868 | 0.84 | 0.86 | 108 | GOL |
| 2 | 574 | 0.69 | 0.78 | 63 | empty |
| 3 | 197 | 0.56 | 0.79 | 26 | empty |
| 4 | 98 | 0.49 | 0.81 | 20 | empty |
| 5 | 177 | 0.45 | 0.75 | 24 | empty |
Interfaces
14 interfaces between chains.
- B–C · 773 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 592 Ų buried · 8 hydrogen bonds · protein-protein
- F–H · 510 Ų buried · 6 hydrogen bonds · protein-protein
- E–G · 492 Ų buried · 5 hydrogen bonds · protein-protein
- C–F · 473 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3FS7 · Crystal structure of Gallus gallus beta-parvalbumin (avian thymic hormone) · the same entry in another collection · chain H against H, TM-score 1.00
- P19753 · AlphaFold monomer V2.0 prediction for parvalbumin, thymic (P19753) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P19753
- Elsewhere: RCSB PDB 3FS7 · PDBe 3FS7 · UniProt P19753
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