MolNFT v1 · #114390 · protein

Crystal structure of a human JAG1 fragment in complex with an anti- JAG1 Fab

5BO1 · Protein jagged-1: “Crystal structure of a human JAG1 fragment in complex with an anti- JAG1 Fab”. X-ray diffraction, 11 pockets (best druggability 0.60). MolNFT v1 #114390 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 5BO1
Type: protein
Length: 1,154 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein jagged-1; Fab heavy chain; Fab light chain
UniProt: P78504
Pockets: 11 · best druggability 0.60

Structure

x-ray diffraction · 4 distinct chains · 4% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein jagged-1	protein	150	3% helix, 31% strand	P78504
H	Fab heavy chain	protein	213	3% helix, 51% strand	—
I	Fab heavy chain	protein	213	4% helix, 50% strand	—
L, M	Fab light chain	protein	214	4% helix, 51% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	491	0.60	0.74	53	empty
2	384	0.56	0.74	56	empty
3	202	0.54	0.78	30	empty
4	268	0.54	0.76	34	empty
5	170	0.54	0.80	27	empty

Interfaces

7 interfaces between chains.

I–M · 1718 Å² buried · 13 hydrogen bonds · protein-protein
H–L · 1687 Å² buried · 9 hydrogen bonds · protein-protein
A–I · 618 Å² buried · 10 hydrogen bonds · protein-protein
B–H · 587 Å² buried · 9 hydrogen bonds · protein-protein
B–L · 563 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 34 disulfide (disulfide).

Compared structures

5BO1 · Crystal structure of a human Jag1 fragment in complex with an anti-Jag1 Fab · the same entry in another collection · chain H against H, TM-score 1.00
P78504 · AlphaFold monomer V2.0 prediction for protein jagged-1 (P78504) · a predicted model of the same protein · chain A against A, TM-score 0.76

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 P78504
Elsewhere: RCSB PDB 5BO1 · PDBe 5BO1 · UniProt P78504

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.