MolNFT v1 · #70058 · protein
Crystal structure of the human NOTCH1 negative regulatory region (nrr) bound to the Fab fragment of an antagonist antibody
3L95 · Anti-NRR1 Fab fragment light chain: “Crystal structure of the human NOTCH1 negative regulatory region (nrr) bound to the Fab fragment of an…”. X-ray diffraction, 3 ligands (NAG, CA, SO4), 17 pockets (best druggability 0.76). MolNFT…
- 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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