Research workbench
Crystal structure of human SP100 phd-bromodomain in the free state
Analyse Crystal structure of human SP100 phd-bromodomain in the free state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PTB
- Type
- protein
- Length
- 345 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear autoantigen sp-100
- UniProt
- H0Y4R8
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear autoantigen sp-100 | protein | 178 | 50% helix, 6% strand | H0Y4R8 |
| B | Nuclear autoantigen sp-100 | protein | 167 | 51% helix, 6% strand | H0Y4R8 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, 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
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 | 226 | 0.59 | 0.80 | 25 | MES |
| 2 | 66 | 0.46 | 0.83 | 16 | empty |
| 3 | 136 | 0.46 | 0.77 | 23 | EDO |
| 4 | 70 | 0.38 | 0.78 | 18 | empty |
| 5 | 87 | 0.33 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 532 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4PTB · Crystal structure of human SP100 PHD-Bromodomain in the free state · 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 H0Y4R8
- Elsewhere: RCSB PDB 4PTB · PDBe 4PTB · UniProt H0Y4R8
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