MolNFT v1 · #169981 · protein
Structure of the NOTCH3 nrr in complex with an antibody Fab fragment
6XSW · Anti-N3 Fab heavy chain: “Structure of the NOTCH3 nrr in complex with an antibody Fab fragment”. X-ray diffraction, 2 ligands (NAG, CA), 20 pockets (best druggability 0.72). MolNFT v1 #169981 on GenesisL1: 3D structure, binding…
- 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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