Research workbench
The complex structure of JMJD2A and trimethylated H3K36 peptide
Analyse The complex structure of JMJD2A and trimethylated H3K36 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P5B
- Type
- protein
- Length
- 715 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jmjc domain-containing histone demethylation protein 3A; Histone H3
- EC
- 1.14.11.-
- UniProt
- O75164, P84239
- Ligands
- OGA, ZN, FE2, OXY
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Jmjc domain-containing histone demethylation protein 3A (EC 1.14.11.-) | protein | 347 | 29% helix, 25% strand | O75164 |
| B | Jmjc domain-containing histone demethylation protein 3A (EC 1.14.11.-) | protein | 337 | 30% helix, 26% strand | O75164 |
| I | Histone H3 | protein | 17 | 0% helix, 12% strand | P84239 |
| J | Histone H3 | protein | 14 | 0% helix, 7% strand | P84239 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, I, B, J
- ZN · Zinc ion · metal · 2 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · 3 copies · chains A, I, B, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.81 | 0.99 | 27 | FE2, OGA, OXY |
| 2 | 120 | 0.80 | 0.98 | 26 | FE2, OGA, OXY |
| 3 | 526 | 0.64 | 0.76 | 60 | empty |
| 4 | 453 | 0.63 | 0.76 | 50 | empty |
| 5 | 66 | 0.46 | 0.83 | 21 | empty |
Interfaces
5 interfaces between chains.
- A–I · 1088 Ų buried · 17 hydrogen bonds · protein-protein
- B–J · 974 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 491 Ų buried · 2 hydrogen bonds · protein-protein
- B–I · 189 Ų buried · 3 hydrogen bonds · protein-protein
- I–J · 67 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (methylation).
Compared structures
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 P84239
- Elsewhere: RCSB PDB 2P5B · PDBe 2P5B · UniProt O75164 · UniProt P84239
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