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Crystal structure of human NO66
Analyse Crystal structure of human NO66 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DIQ
- Type
- protein
- Length
- 916 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine-specific demethylase NO66
- EC
- 1.14.11.27
- UniProt
- Q9H6W3
- Ligands
- PD2, NI, SO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine-specific demethylase NO66 (EC 1.14.11.27) | protein | 459 | 38% helix, 22% strand | Q9H6W3 |
| B | Lysine-specific demethylase NO66 (EC 1.14.11.27) | protein | 457 | 38% helix, 22% strand | Q9H6W3 |
Ligands and binding sites
- PD2 · Pyridine-2,4-dicarboxylic acid · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.73 | 0.88 | 40 | empty |
| 2 | 395 | 0.68 | 0.81 | 67 | NI, PD2 |
| 3 | 367 | 0.68 | 0.82 | 62 | NI, PD2 |
| 4 | 433 | 0.66 | 0.79 | 61 | empty |
| 5 | 106 | 0.38 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 3376 Ų buried · 53 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 Q9H6W3
- Elsewhere: RCSB PDB 4DIQ · PDBe 4DIQ · UniProt Q9H6W3
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