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Crystal structure of the human NOTCH1 negative regulatory region (nrr) bound to the Fab fragment of an antagonist antibody
Analyse Crystal structure of the human NOTCH1 negative regulatory region (nrr) bound to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L95
- Type
- protein
- Length
- 1,308 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-NRR1 Fab fragment light chain; Anti-NRR1 Fab fragment heavy chain; Neurogenic locus…
- UniProt
- P46531
- Ligands
- NAG, CA, SO4
- Pockets
- 17 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | Anti-NRR1 Fab fragment light chain | protein | 212 | 7% helix, 51% strand | — |
| B | Anti-NRR1 Fab fragment heavy chain | protein | 220 | 7% helix, 53% strand | — |
| X | Neurogenic locus notch homolog protein 1 | protein | 230 | 34% helix, 14% strand | P46531 |
| H | Anti-NRR1 Fab fragment heavy chain | protein | 219 | 4% helix, 50% strand | — |
| Y | Neurogenic locus notch homolog protein 1 | protein | 215 | 34% helix, 15% strand | P46531 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains X
- CA · Calcium ion · metal · 6 copies · chains X, B, Y, H
- SO4 · Sulfate ion · ion · chains B, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 276 | 0.76 | 0.89 | 32 | empty |
| 2 | 361 | 0.74 | 0.85 | 30 | empty |
| 3 | 574 | 0.69 | 0.79 | 49 | empty |
| 4 | 542 | 0.65 | 0.76 | 55 | empty |
| 5 | 662 | 0.63 | 0.74 | 67 | empty |
Interfaces
8 interfaces between chains.
- L–H · 1907 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1825 Ų buried · 13 hydrogen bonds · protein-protein
- B–X · 612 Ų buried · 14 hydrogen bonds · protein-protein
- H–Y · 610 Ų buried · 14 hydrogen bonds · protein-protein
- X–Y · 562 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3L95 · Crystal structure of the human Notch1 Negative Regulatory Region (NRR) bound to the fab… · the same entry in another collection · chain Y against Y, 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 Y against A, TM-score 0.95
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 3L95 · PDBe 3L95 · UniProt P46531
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