Research workbench

CD47-diabody complex

Analyse CD47-diabody complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5IWL
Type: protein
Length: 694 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5F9 diabody; Leukocyte surface antigen CD47
UniProt: Q08722
Ligands: NAG
Pockets: 8 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	5F9 diabody	protein	233	4% helix, 51% strand	—
C, D	Leukocyte surface antigen CD47	protein	114	11% helix, 48% strand	Q08722

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains C, D
PGE · Triethylene glycol · additive · 2 copies · chains B, A, C, D

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

Pockets

8 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	514	0.67	0.78	50	empty
2	149	0.46	0.77	29	empty
3	137	0.43	0.76	24	empty
4	97	0.38	0.76	23	empty
5	87	0.35	0.74	24	empty

Interfaces

5 interfaces between chains.

B–A · 2035 Å² buried · 22 hydrogen bonds · protein-protein
B–C · 424 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 421 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 387 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 364 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 6 glycan, 4 modified (disulfide, N-glycosylation, cyclization).

Compared structures

5IWL · CD47-diabody complex · the same entry in another collection · chain B against B, TM-score 1.00
Q08722 · AlphaFold monomer V2.0 prediction for leukocyte surface antigen CD47 (Q08722) · a predicted model of the same protein · chain D 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 5IWL · PDBe 5IWL · UniProt Q08722

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