MolNFT v1 · #126283 · protein
JMJD2A/ KDM4A complexed with NI(II) and macrocyclic peptide inhibitor CP2 (13-mer)
5LY1 · Lysine-specific demethylase 4A: “JMJD2A/ KDM4A complexed with NI(II) and macrocyclic peptide inhibitor CP2 (13-mer)”. X-ray diffraction, 4 ligands (48V, NI, ZN), 19 pockets (best druggability 0.77). MolNFT v1 #126283 on GenesisL1…
- PDB
- 5LY1
- Type
- protein
- Length
- 1,397 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A; CP2
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- 48V, NI, ZN, CL
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 349 | 31% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 346 | 33% helix, 25% strand | O75164 |
| C | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 342 | 31% helix, 25% strand | O75164 |
| D | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 347 | 34% helix, 24% strand | O75164 |
| E | CP2 | protein | 13 | 0% helix, 62% strand | — |
Ligands and binding sites
- 48V · {[(2R)-2,3-diamino-3-oxopropyl]sulfanyl}acetic acid · ligand · chains D, E
- NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, E, D
- CL · Chloride ion · ion · 3 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C
- PPI · Propanoic acid · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.77 | 0.98 | 24 | NI |
| 2 | 742 | 0.77 | 0.81 | 77 | NI, PPI |
| 3 | 837 | 0.75 | 0.79 | 80 | NI, CL, PPI |
| 4 | 455 | 0.71 | 0.81 | 47 | NI, PPI |
| 5 | 347 | 0.67 | 0.80 | 27 | empty |
Interfaces
6 interfaces between chains.
- C–E · 859 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 545 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 540 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 329 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 329 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 d-amino (covalent ligand, D-amino acid).
Compared structures
- 5LY1 · JMJD2A/ KDM4A COMPLEXED WITH NI(II) AND Macrocyclic PEPTIDE Inhibitor CP2 (13-mer) · 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 5LY1 · PDBe 5LY1 · UniProt O75164
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