Research workbench
Crystal structure of NOTCH3 nrr in complex with 20358 Fab
Analyse Crystal structure of NOTCH3 nrr in complex with 20358 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CZX
- Type
- protein
- Length
- 1,309 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neurogenic locus notch homolog protein 3; 20358 Fab heavy chain; 20358 Fab light chain
- UniProt
- Q9UM47
- Ligands
- NAG, CA, CL
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neurogenic locus notch homolog protein 3 | protein | 227 | 31% helix, 15% strand | Q9UM47 |
| C | 20358 Fab heavy chain | protein | 214 | 8% helix, 54% strand | — |
| D, L | 20358 Fab light chain | protein | 213 | 6% helix, 51% strand | — |
| H | 20358 Fab heavy chain | protein | 215 | 9% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, L, B, D
- CA · Calcium ion · metal · 6 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains C, H, L
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, H, L, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 658 | 0.80 | 0.85 | 72 | EDO |
| 2 | 467 | 0.80 | 0.87 | 50 | EDO |
| 3 | 744 | 0.77 | 0.81 | 108 | EDO |
| 4 | 181 | 0.51 | 0.78 | 29 | empty |
| 5 | 157 | 0.50 | 0.78 | 31 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1685 Ų buried · 13 hydrogen bonds · protein-protein
- H–L · 1684 Ų buried · 16 hydrogen bonds · protein-protein
- D–L · 782 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 565 Ų buried · 7 hydrogen bonds · protein-protein
- A–H · 552 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5CZX · Crystal structure of Notch3 NRR in complex with 20358 Fab · the same entry in another collection · chain C against C, TM-score 1.00
- Q9UM47 · AlphaFold monomer V2.0 prediction for neurogenic locus notch homolog protein 3 (Q9UM47) · 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 Q9UM47
- Elsewhere: RCSB PDB 5CZX · PDBe 5CZX · UniProt Q9UM47
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