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PanDDA analysis group deposition -- Crystal Structure of SP100 after initial refinement with no ligand modelled (structure 43)
Analyse PanDDA analysis group deposition -- Crystal Structure of SP100 after initial… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5PXJ
- Type
- protein
- Length
- 355 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.68
- Source
- Homo sapiens
- Molecule
- Nuclear autoantigen Sp-100
- UniProt
- P23497
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · resolution 1.68 · 2 distinct chains · 48% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear autoantigen Sp-100 | protein | 178 | 50% helix, 5% strand | P23497 |
| B | Nuclear autoantigen Sp-100 | protein | 177 | 47% helix, 6% strand | P23497 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.59 | 0.80 | 26 | MES |
| 2 | 157 | 0.43 | 0.75 | 20 | EDO |
| 3 | 99 | 0.35 | 0.74 | 16 | empty |
| 4 | 88 | 0.32 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 532 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5PXJ · Pandda analysis group deposition -- crystal structure of SP100 after initial refinement… · the same entry in another collection · chain A against A, TM-score 1.00
- P23497 · AlphaFold monomer V2.0 prediction for nuclear autoantigen sp-100 (P23497) · a predicted model of the same protein · chain B against A, TM-score 0.36
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 P23497
- Elsewhere: RCSB PDB 5PXJ · PDBe 5PXJ · UniProt P23497
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