MolNFT v1 · #54728 · protein
Crystal structure of the human JMJD3 jumonji domain
2XXZ · Lysine-specific demethylase 6B: “Crystal structure of the human JMJD3 jumonji domain”. X-ray diffraction, 3 ligands (8XQ, NI, NA), 5 pockets (best druggability 0.64). MolNFT v1 #54728 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2XXZ
- Type
- protein
- Length
- 578 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 6B
- EC
- 1.14.11.-
- UniProt
- O15054
- Ligands
- 8XQ, NI, NA
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 6B (EC 1.14.11.-) | protein | 292 | 28% helix, 30% strand | O15054 |
| B | Lysine-specific demethylase 6B (EC 1.14.11.-) | protein | 286 | 33% helix, 30% strand | O15054 |
Ligands and binding sites
- 8XQ · 8-hydroxyquinoline-5-carboxylic acid · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 3 copies · chains A, B
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 509 | 0.64 | 0.76 | 48 | EDO |
| 2 | 315 | 0.63 | 0.80 | 35 | NI, 8XQ |
| 3 | 279 | 0.62 | 0.80 | 36 | NI, 8XQ |
| 4 | 65 | 0.38 | 0.78 | 15 | EDO |
| 5 | 52 | 0.28 | 0.75 | 14 | EDO |
Interfaces
1 interface between chains.
- A–B · 900 Ų buried · 13 hydrogen bonds · protein-protein
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 O15054
- Elsewhere: RCSB PDB 2XXZ · PDBe 2XXZ · UniProt O15054
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