Research workbench
Structure of lnr-hd (negative regulatory region) from human notch 2
Analyse Structure of lnr-hd (negative regulatory region) from human notch 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OO4
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurogenic locus notch homolog protein 2
- UniProt
- Q04721
- Ligands
- CA, ZN
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neurogenic locus notch homolog protein 2 | protein | 226 | 34% helix, 16% strand | Q04721 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B
- ZN · Zinc ion · metal · chains A
- GOL · Glycerol · additive · 10 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.75 | 0.79 | 68 | GOL |
| 2 | 223 | 0.57 | 0.79 | 45 | empty |
| 3 | 186 | 0.45 | 0.75 | 26 | empty |
| 4 | 85 | 0.37 | 0.76 | 23 | GOL |
| 5 | 73 | 0.30 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 440 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 disulfide (disulfide).
Compared structures
- 2OO4 · Structure of LNR-HD (Negative Regulatory Region) from human Notch 2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q04721 · AlphaFold monomer V2.0 prediction for neurogenic locus notch homolog protein 2 (Q04721) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q04721
- Elsewhere: RCSB PDB 2OO4 · PDBe 2OO4 · UniProt Q04721
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