Research workbench
Crystal structure of the S1-cleaved NOTCH1 negative regulatory region (nrr)
Analyse Crystal structure of the S1-cleaved NOTCH1 negative regulatory region (nrr) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3I08
- Type
- protein
- Length
- 466 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurogenic locus notch homolog protein 1
- UniProt
- P46531
- Ligands
- CA, CL
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Neurogenic locus notch homolog protein 1 | protein | 174 | 39% helix, 11% strand | P46531 |
| B | Neurogenic locus notch homolog protein 1 | protein | 60 | 28% helix, 30% strand | P46531 |
| D | Neurogenic locus notch homolog protein 1 | protein | 58 | 29% helix, 28% strand | P46531 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.70 | 0.96 | 32 | empty |
| 2 | 183 | 0.53 | 0.78 | 32 | empty |
| 3 | 198 | 0.52 | 0.77 | 34 | empty |
| 4 | 124 | 0.46 | 0.78 | 24 | empty |
| 5 | 127 | 0.46 | 0.78 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 3226 Ų buried · 56 hydrogen bonds · protein-protein
- C–D · 3210 Ų buried · 56 hydrogen bonds · protein-protein
- A–C · 475 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 241 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 127 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 3I08 · Crystal structure of the S1-cleaved Notch1 Negative Regulatory Region (NRR) · the same entry in another collection · chain A against A, TM-score 1.00
- P46531 · AlphaFold monomer V2.0 prediction for neurogenic locus notch homolog protein 1 (P46531) · 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 P46531
- Elsewhere: RCSB PDB 3I08 · PDBe 3I08 · UniProt P46531
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