Research workbench
Crystal structure of double tudor domain of human lysine demethylase KDM4A
Analyse Crystal structure of double tudor domain of human lysine demethylase KDM4A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5D6W
- Type
- protein
- Length
- 460 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- SRT
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 115 | 9% helix, 51% strand | O75164 |
Ligands and binding sites
- SRT · S,R meso-tartaric acid · ligand · 4 copies · chains A, B, C, D
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 | 307 | 0.53 | 0.74 | 48 | empty |
| 2 | 96 | 0.37 | 0.75 | 22 | empty |
| 3 | 77 | 0.32 | 0.75 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–C · 815 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 416 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 401 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 346 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5D6W · Crystal structure of double tudor domain of human lysine demethylase KDM4A · 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 O75164
- Elsewhere: RCSB PDB 5D6W · PDBe 5D6W · UniProt O75164
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