MolNFT v1 · #131130 · protein
Pandda analysis group deposition -- crystal structure of SP100 in complex with N09600B
5PWD · Nuclear autoantigen sp-100: “Pandda analysis group deposition -- crystal structure of SP100 in complex with N09600B”. X-ray diffraction, 3 ligands (81P, ZN, CL), 2 pockets (best druggability 0.64). MolNFT v1 #131130 on GenesisL1: 3D…
- PDB
- 5PWD
- 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
- 81P, ZN, CL
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 50% 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 | 49% helix, 5% strand | P23497 |
Ligands and binding sites
- 81P · 4-(methylamino)benzoic acid · ligand · chains B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 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
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 396 | 0.64 | 0.78 | 48 | MES, CL, EDO |
| 2 | 80 | 0.32 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 533 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5PWD · PanDDA analysis group deposition -- Crystal Structure of SP100 in complex with N09600b · 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 5PWD · PDBe 5PWD · UniProt P23497
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