Research workbench
Structure of the NOTCH3 nrr in complex with an antibody Fab fragment
Analyse Structure of the NOTCH3 nrr in complex with an antibody Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XSW
- Type
- protein
- Length
- 2,508 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-N3 Fab heavy chain; Anti-N3 Fab light chain; Neurogenic locus notch homolog protein 3
- UniProt
- Q9UM47
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 12 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anti-N3 Fab heavy chain | protein | 215 | 7% helix, 50% strand | — |
| B | Anti-N3 Fab light chain | protein | 211 | 7% helix, 50% strand | — |
| C | Neurogenic locus notch homolog protein 3 | protein | 220 | 35% helix, 15% strand | Q9UM47 |
| D | Anti-N3 Fab heavy chain | protein | 184 | 7% helix, 49% strand | — |
| E | Anti-N3 Fab light chain | protein | 144 | 5% helix, 37% strand | — |
| F | Neurogenic locus notch homolog protein 3 | protein | 229 | 29% helix, 14% strand | Q9UM47 |
| G | Anti-N3 Fab heavy chain | protein | 215 | 6% helix, 53% strand | — |
| H | Anti-N3 Fab heavy chain | protein | 217 | 7% helix, 50% strand | — |
| I | Anti-N3 Fab light chain | protein | 211 | 6% helix, 50% strand | — |
| J | Neurogenic locus notch homolog protein 3 | protein | 218 | 33% helix, 16% strand | Q9UM47 |
| L | Anti-N3 Fab light chain | protein | 213 | 7% helix, 51% strand | — |
| X | Neurogenic locus notch homolog protein 3 | protein | 231 | 36% helix, 15% strand | Q9UM47 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains X, L, C, F
- CA · Calcium ion · metal · 13 copies · chains C, F, J, X
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.72 | 0.78 | 96 | empty |
| 2 | 83 | 0.69 | 0.94 | 20 | empty |
| 3 | 488 | 0.65 | 0.77 | 42 | empty |
| 4 | 400 | 0.65 | 0.79 | 52 | empty |
| 5 | 61 | 0.65 | 0.94 | 19 | empty |
Interfaces
21 interfaces between chains.
- H–L · 1846 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1757 Ų buried · 11 hydrogen bonds · protein-protein
- G–I · 1757 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1216 Ų buried · 7 hydrogen bonds · protein-protein
- I–J · 683 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6XSW · Structure of the Notch3 NRR in complex with an antibody Fab Fragment · the same entry in another collection · chain X against X, TM-score 1.00
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 6XSW · PDBe 6XSW · UniProt Q9UM47
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