MolNFT v1 · #94176 · protein
Crystal structure of human JMJD2D/KDM4D apoenzyme
4HOO · Lysine-specific demethylase 4D: “Crystal structure of human JMJD2D/KDM4D apoenzyme”. X-ray diffraction, 2 ligands (NI, ZN), 7 pockets (best druggability 0.73). MolNFT v1 #94176 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 4HOO
- Type
- protein
- Length
- 657 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase 4D
- EC
- 1.14.11.-
- UniProt
- Q6B0I6
- Ligands
- NI, ZN
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase 4D (EC 1.14.11.-) | protein | 327 | 27% helix, 26% strand | Q6B0I6 |
| B | Lysine-specific demethylase 4D (EC 1.14.11.-) | protein | 330 | 31% helix, 25% strand | Q6B0I6 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.73 | 0.85 | 39 | NI |
| 2 | 376 | 0.71 | 0.83 | 43 | NI |
| 3 | 256 | 0.61 | 0.80 | 17 | empty |
| 4 | 117 | 0.52 | 0.81 | 19 | empty |
| 5 | 125 | 0.50 | 0.80 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 642 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4HOO · Crystal structure of human JMJD2D/KDM4D apoenzyme · 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 Q6B0I6
- Elsewhere: RCSB PDB 4HOO · PDBe 4HOO · UniProt Q6B0I6
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