Research workbench
P107 pocket domain complexed with HDAC1 peptide
Analyse P107 pocket domain complexed with HDAC1 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SME
- Type
- protein
- Length
- 352 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoblastoma-like protein 1; Histone deacetylase 1
- EC
- 3.5.1.98, 3.5.1.-
- UniProt
- P28749, Q13547
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 63% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoblastoma-like protein 1 | protein | 342 | 65% helix, 1% strand | P28749 |
| B | Histone deacetylase 1 (EC 3.5.1.98, 3.5.1.-) | protein | 10 | 0% helix, 0% strand | Q13547 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.41 | 0.75 | 19 | empty |
| 2 | 97 | 0.34 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 575 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7SME · p107 pocket domain complexed with HDAC1 peptide · the same entry in another collection · chain A against A, TM-score 1.00
- P28749 · AlphaFold monomer V2.0 prediction for retinoblastoma-like protein 1 (P28749) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q13547 · AlphaFold monomer V2.0 prediction for histone deacetylase 1 (Q13547) · a predicted model of the same protein · chain B against A, TM-score 0.42
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 P28749
- Every structure of UniProt Q13547
- Elsewhere: RCSB PDB 7SME · PDBe 7SME · UniProt P28749 · UniProt Q13547
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