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Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23ME3
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
- 5D6Y
- Type
- protein
- Length
- 671 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A; Peptide H3K23ME3 (19-28)
- EC
- 1.14.11.-
- UniProt
- O75164
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 5 distinct chains · 9% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, F | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 108 | 9% helix, 58% strand | O75164 |
| a, b | Peptide H3K23ME3 (19-28) | protein | 9 | 0% helix, 22% strand | — |
| C, D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 104 | 10% helix, 58% strand | O75164 |
| c, d | Peptide H3K23ME3 (19-28) | protein | 7 | 0% helix, 29% strand | — |
| E | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 107 | 9% helix, 54% strand | O75164 |
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.74 | 0.85 | 47 | empty |
| 2 | 172 | 0.63 | 0.84 | 34 | empty |
| 3 | 187 | 0.62 | 0.83 | 34 | empty |
| 4 | 238 | 0.57 | 0.78 | 32 | empty |
| 5 | 257 | 0.56 | 0.78 | 33 | empty |
Interfaces
22 interfaces between chains.
- E–F · 1200 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 1083 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1074 Ų buried · 21 hydrogen bonds · protein-protein
- B–b · 554 Ų buried · 6 hydrogen bonds · protein-protein
- A–a · 552 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
- 5D6Y · Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with… · 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 5D6Y · PDBe 5D6Y · UniProt O75164
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