Research workbench

Complex of high-affinity sirp alpha variant FD6 with CD47

Analyse Complex of high-affinity sirp alpha variant FD6 with CD47 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KJY
Type: protein
Length: 458 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Leukocyte surface antigen CD47; High-affinity sirpa variant FD6
UniProt: Q08722
Ligands: NAG, SO4
Pockets: 3 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Leukocyte surface antigen CD47	protein	114	12% helix, 46% strand	Q08722
B	High-affinity sirpa variant FD6	protein	114	3% helix, 40% strand	—
D	High-affinity sirpa variant FD6	protein	116	3% helix, 41% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C
SO4 · Sulfate ion · ion · 3 copies · chains A, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	573	0.62	0.74	59	SO4
2	70	0.32	0.75	19	empty
3	65	0.28	0.73	18	empty

Interfaces

4 interfaces between chains.

A–B · 943 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 937 Å² buried · 21 hydrogen bonds · protein-protein
B–D · 281 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 175 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 glycan, 4 disulfide, 2 modified (N-glycosylation, disulfide, cyclization).

Compared structures

4KJY · Complex of high-affinity SIRP alpha variant FD6 with CD47 · the same entry in another collection · chain A against A, TM-score 1.00
Q08722 · AlphaFold monomer V2.0 prediction for leukocyte surface antigen CD47 (Q08722) · a predicted model of the same protein · chain C against A, TM-score 0.99

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 Q08722
Elsewhere: RCSB PDB 4KJY · PDBe 4KJY · UniProt Q08722

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