MolNFT v1 · #175009 · protein
Crystal structure of LSD1-corest in complex with prsflvrrp peptide
7CDC · Lysine-specific histone demethylase 1A: “Crystal structure of LSD1-corest in complex with prsflvrrp peptide”. X-ray diffraction, 1 ligand (FAD), 10 pockets (best druggability 0.84). MolNFT v1 #175009 on GenesisL1: 3D structure…
- PDB
- 7CDC
- Type
- protein
- Length
- 802 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific histone demethylase 1A; Rest corepressor 1…
- EC
- 1.14.99.66
- UniProt
- O60341, Q9UKL0
- Ligands
- FAD
- Pockets
- 10 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific histone demethylase 1A (EC 1.14.99.66) | protein | 661 | 44% helix, 16% strand | O60341 |
| B | Rest corepressor 1 | protein | 132 | 64% helix, 0% strand | Q9UKL0 |
| C | Pro-arg-ser-phe-leu-val-arg-arg-pro | protein | 9 | 33% helix, 0% strand | — |
Ligands and binding sites
- 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
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 422 | 0.84 | 0.92 | 73 | FAD |
| 2 | 351 | 0.64 | 0.79 | 31 | empty |
| 3 | 78 | 0.43 | 0.79 | 19 | empty |
| 4 | 57 | 0.41 | 0.82 | 24 | empty |
| 5 | 91 | 0.37 | 0.76 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2668 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 884 Ų buried · 15 hydrogen bonds · protein-protein
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 7CDC · PDBe 7CDC · UniProt O60341 · UniProt Q9UKL0
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