MolNFT v1 · #149615 · protein
Crystal structure of human SP100 in complex with bromodomain-focused fragment XS039818E 1-(3-phenyl-1,2,4-oxadiazol-5-YL)METHANAMINE
6G5N · Nuclear autoantigen sp-100: “Crystal structure of human SP100 in complex with bromodomain-focused fragment XS039818E…”. X-ray diffraction, 3 ligands (ENK, ZN, CL), 3 pockets (best druggability 0.60). MolNFT v1 #149615 on GenesisL1…
- PDB
- 6G5N
- Type
- protein
- Length
- 346 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear autoantigen sp-100
- UniProt
- P23497
- Ligands
- ENK, ZN, CL
- Pockets
- 3 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear autoantigen sp-100 | protein | 177 | 50% helix, 6% strand | P23497 |
| B | Nuclear autoantigen sp-100 | protein | 169 | 49% helix, 6% strand | P23497 |
Ligands and binding sites
- ENK · (3-phenyl-1,2,4-oxadiazol-5-yl)methanamine · ligand · chains A
- ZN · Zinc ion · metal · 4 copies · chains A, B
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 4 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.60 | 0.81 | 25 | MES, EDO |
| 2 | 171 | 0.49 | 0.77 | 29 | EDO |
| 3 | 67 | 0.30 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 541 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6G5N · Crystal structure of human SP100 in complex with bromodomain-focused fragment XS039818e… · 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 6G5N · PDBe 6G5N · UniProt P23497
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