Research workbench
JMJD2A/ KDM4A complexed with NI(II), nog and macrocyclic peptide inhibitor CP2_R6KME3 (13-mer)
Analyse JMJD2A/ KDM4A complexed with NI(II), nog and macrocyclic peptide inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LY2
- Type
- protein
- Length
- 1,424 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A; CP2_R6KME3
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- OGA, 48V, NI, ZN, CL
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 30% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 348 | 30% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 345 | 31% helix, 24% strand | O75164 |
| C | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 342 | 30% helix, 25% strand | O75164 |
| D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 347 | 31% helix, 24% strand | O75164 |
| E, G | CP2_R6KME3 | protein | 13 | 0% helix, 62% strand | — |
| F, H | CP2_R6KME3 | protein | 8 | 0% helix, 50% strand | — |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 4 copies · chains A, E, B, F, C, G, D, H
- 48V · {[(2R)-2,3-diamino-3-oxopropyl]sulfanyl}acetic acid · ligand · 2 copies · chains B, E, F, D, G, H
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, F, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, E, B, F, C, G, D, H
- CL · Chloride ion · ion · 5 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.78 | 0.98 | 25 | NI, OGA |
| 2 | 90 | 0.76 | 0.98 | 23 | NI, OGA |
| 3 | 83 | 0.76 | 0.98 | 21 | NI, OGA |
| 4 | 763 | 0.76 | 0.81 | 86 | GOL |
| 5 | 78 | 0.74 | 0.97 | 22 | NI, OGA |
Interfaces
13 interfaces between chains.
- C–G · 859 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 858 Ų buried · 11 hydrogen bonds · protein-protein
- D–H · 741 Ų buried · 6 hydrogen bonds · protein-protein
- B–F · 698 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 548 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified, 2 d-amino (covalent ligand, methylation, D-amino acid).
Compared structures
- 5LY2 · JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Macrocyclic PEPTIDE Inhibitor CP2_R6Kme3… · 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 5LY2 · PDBe 5LY2 · UniProt O75164
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