Research workbench
Crystal structure of human JMJD2A in complex with pyruvate
Analyse Crystal structure of human JMJD2A in complex with pyruvate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FYI
- Type
- protein
- Length
- 695 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4A
- EC
- 1.14.11.-
- UniProt
- O75164
- Ligands
- PYR, 1KA, NI, ZN
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 351 | 31% helix, 24% strand | O75164 |
| B | Lysine-specific demethylase 4A (EC 1.14.11.-) | protein | 344 | 31% helix, 25% strand | O75164 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 4 copies · chains A, B
- 1KA · (2-hydroxyethoxy)acetaldehyde · ligand · chains B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 17 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 434 | 0.74 | 0.84 | 42 | NI, PYR, EDO |
| 2 | 398 | 0.71 | 0.82 | 38 | NI, PYR, EDO |
| 3 | 622 | 0.66 | 0.76 | 64 | EDO, 1KA |
| 4 | 111 | 0.55 | 0.83 | 24 | EDO |
| 5 | 108 | 0.49 | 0.80 | 23 | EDO |
Interfaces
1 interface between chains.
- A–B · 421 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5FYI · Crystal structure of human JMJD2A in complex with pyruvate · 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 5FYI · PDBe 5FYI · UniProt O75164
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