MolNFT v1 · #115984 · protein

Crystal structure of NOTCH3 nrr in complex with 20350 Fab

5CZV · Neurogenic locus notch homolog protein 3: “Crystal structure of NOTCH3 nrr in complex with 20350 Fab”. X-ray diffraction, 2 ligands (NAG, CA), 6 pockets (best druggability 0.58). MolNFT v1 #115984 on GenesisL1: 3D structure, binding…

PDB: 5CZV
Type: protein
Length: 642 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neurogenic locus notch homolog protein 3; Fab 20350 heavy chain; Fab 20350 light chain
UniProt: Q9UM47
Ligands: NAG, CA
Pockets: 6 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 17% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Neurogenic locus notch homolog protein 3	protein	225	33% helix, 16% strand	Q9UM47
H	Fab 20350 heavy chain	protein	206	9% helix, 47% strand	—
L	Fab 20350 light chain	protein	211	6% helix, 51% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
CA · Calcium ion · metal · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.58	0.91	19	empty
2	331	0.55	0.75	41	empty
3	148	0.52	0.80	19	empty
4	108	0.37	0.74	22	empty
5	100	0.35	0.73	21	empty

Interfaces

3 interfaces between chains.

H–L · 1720 Å² buried · 17 hydrogen bonds · protein-protein
A–H · 675 Å² buried · 7 hydrogen bonds · protein-protein
A–L · 595 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

5CZV · Crystal structure of Notch3 NRR in complex with 20350 Fab · the same entry in another collection · chain A against A, 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 0.97

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 5CZV · PDBe 5CZV · UniProt Q9UM47

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