MolNFT v1 · #119450 · protein
JMJD2A complexed with NI(II), nog and histone H4(1-15)R3ME2S peptide
5FWE · Lysine-specific demethylase 4A: “JMJD2A complexed with NI(II), nog and histone H4(1-15)R3ME2S peptide”. X-ray diffraction, 4 ligands (OGA, NI, ZN), 10 pockets (best druggability 0.73). MolNFT v1 #119450 on GenesisL1: 3D structure…
- PDB
- 5FWE
- Type
- protein
- Length
- 706 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A; Synthetic peptide
- EC
- 1.14.11.-
- UniProt
- O75164, P62805
- Ligands
- OGA, NI, ZN, CL
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 348 | 31% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 353 | 33% helix, 24% strand | O75164 |
| C | Synthetic peptide | protein | 2 | 0% helix, 0% strand | P62805 |
| D | Synthetic peptide | protein | 3 | 0% helix, 0% strand | P62805 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, B, D
- NI · Nickel (II) ion · metal · 2 copies · chains A, B, D
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.73 | 0.84 | 39 | NI, OGA |
| 2 | 63 | 0.72 | 0.98 | 23 | OGA |
| 3 | 537 | 0.64 | 0.76 | 53 | empty |
| 4 | 112 | 0.52 | 0.82 | 24 | empty |
| 5 | 156 | 0.50 | 0.78 | 24 | empty |
Interfaces
3 interfaces between chains.
- B–D · 382 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 372 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 266 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
- 5FWE · JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3me2s PEPTIDE · 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
- Every structure of UniProt P62805
- Elsewhere: RCSB PDB 5FWE · PDBe 5FWE · UniProt O75164 · UniProt P62805
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