Research workbench
Pandda analysis group deposition -- crystal structure of SP100 in complex with E48115B
Analyse Pandda analysis group deposition -- crystal structure of SP100 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5PWC
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear autoantigen sp-100
- UniProt
- P23497
- Ligands
- W77, ZN, CL
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear autoantigen sp-100 | protein | 174 | 51% helix, 5% strand | P23497 |
| B | Nuclear autoantigen sp-100 | protein | 166 | 50% helix, 5% strand | P23497 |
Ligands and binding sites
- W77 · 2,4-dichloro-N-(pyridin-3-yl)benzamide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 3 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
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 218 | 0.58 | 0.80 | 26 | MES, EDO |
| 2 | 180 | 0.49 | 0.76 | 29 | EDO |
| 3 | 52 | 0.47 | 0.85 | 16 | CL |
| 4 | 61 | 0.39 | 0.79 | 18 | empty |
| 5 | 75 | 0.31 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 530 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5PWC · PanDDA analysis group deposition -- Crystal Structure of SP100 in complex with E48115b · the same entry in another collection · chain A against A, TM-score 1.00
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 5PWC · PDBe 5PWC · UniProt P23497
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.