Research workbench
Crystal structure of human KDM4A complexed with co-substrate analog nog and histone H3 peptide with K9R mutation
Analyse Crystal structure of human KDM4A complexed with co-substrate analog nog and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HGT
- Type
- protein
- Length
- 1,409 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A; Histone H3.3
- EC
- 1.14.11.-
- UniProt
- O75164, P84243
- Ligands
- OGA, ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 350 | 30% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 345 | 30% helix, 25% strand | O75164 |
| C | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 348 | 29% helix, 24% strand | O75164 |
| D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 342 | 30% helix, 25% strand | O75164 |
| E | Histone H3.3 | protein | 7 | 0% helix, 14% strand | P84243 |
| F, G | Histone H3.3 | protein | 6 | 0% helix, 17% strand | P84243 |
| H | Histone H3.3 | protein | 5 | 0% helix, 0% strand | P84243 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- ZN · Zinc ion · metal · 8 copies · chains A, E, B, C, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.78 | 0.98 | 24 | ZN, OGA |
| 2 | 107 | 0.77 | 0.97 | 26 | ZN, OGA |
| 3 | 93 | 0.77 | 0.98 | 22 | ZN, OGA |
| 4 | 87 | 0.75 | 0.97 | 22 | ZN, OGA |
| 5 | 101 | 0.54 | 0.83 | 20 | empty |
Interfaces
7 interfaces between chains.
- A–E · 597 Ų buried · 14 hydrogen bonds · protein-protein
- B–F · 573 Ų buried · 17 hydrogen bonds · protein-protein
- C–G · 549 Ų buried · 17 hydrogen bonds · protein-protein
- D–H · 508 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 301 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6HGT · Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3… · the same entry in another collection · chain G against G, 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
- Every structure of UniProt P84243
- Elsewhere: RCSB PDB 6HGT · PDBe 6HGT · UniProt O75164 · UniProt P84243
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