Research workbench
Crystal structure of LSD1-corest in complex with peptide 13
Analyse Crystal structure of LSD1-corest in complex with peptide 13 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H6R
- Type
- protein
- Length
- 807 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1A; Rest corepressor 1; Peptide…
- EC
- 1.-.-.-
- UniProt
- O60341, Q9UKL0
- Ligands
- HSE, FAD
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.-.-.-) | protein | 662 | 44% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 132 | 62% helix, 0% strand | Q9UKL0 |
| C | Peptide (HSE)RTMQTARKSTGGKAPRKQLK | protein | 13 | 0% helix, 0% strand | — |
Ligands and binding sites
- HSE · L-homoserine · ligand · chains A, C
- FAD · Flavin-adenine dinucleotide · ligand · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 343 | 0.85 | 0.95 | 57 | FAD |
| 2 | 344 | 0.63 | 0.78 | 40 | empty |
| 3 | 81 | 0.43 | 0.79 | 19 | empty |
| 4 | 89 | 0.40 | 0.78 | 23 | GOL |
| 5 | 114 | 0.36 | 0.74 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2684 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1063 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
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 O60341
- Every structure of UniProt Q9UKL0
- Elsewhere: RCSB PDB 5H6R · PDBe 5H6R · UniProt O60341 · UniProt Q9UKL0
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