MolNFT v1 · #116218 · protein
Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23ME3
5D6Y · Lysine-specific demethylase 4A: “Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23ME3”. X-ray diffraction, 9 pockets (best druggability 0.74). MolNFT v1 #116218 on GenesisL1: 3D…
- 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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