MolNFT v1 · #158915 · protein

Anti-CD28XCD3 codv Fab bound to CD28

6O8D · T-cell-specific surface glycoprotein CD28: “Anti-CD28XCD3 codv Fab bound to CD28”. X-ray diffraction, 1 ligand (NAG), 11 pockets (best druggability 0.79). MolNFT v1 #158915 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6O8D
Type: protein
Length: 796 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-cell-specific surface glycoprotein CD28; Anti-CD28XCD3 codv Fab light chain…
UniProt: P10747
Ligands: NAG
Pockets: 11 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 42% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	T-cell-specific surface glycoprotein CD28	protein	115	3% helix, 38% strand	P10747
L	Anti-CD28XCD3 codv Fab light chain	protein	338	4% helix, 39% strand	—
H	Anti-CD28XCD3 codv Fab heavy chain	protein	343	6% helix, 45% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C

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	174	0.79	0.94	24	empty
2	626	0.75	0.81	62	empty
3	505	0.63	0.76	35	empty
4	251	0.59	0.79	35	empty
5	76	0.57	0.87	26	empty

Interfaces

3 interfaces between chains.

L–H · 2860 Å² buried · 27 hydrogen bonds · protein-protein
C–H · 292 Å² buried · 4 hydrogen bonds · protein-protein
C–L · 196 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6O8D · Anti-CD28xCD3 CODV Fab bound to CD28 · the same entry in another collection · chain C against C, TM-score 1.00
P10747 · AlphaFold monomer V2.0 prediction for T-cell-specific surface glycoprotein CD28 (P10747) · a predicted model of the same protein · chain C against A, TM-score 0.89

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 P10747
Elsewhere: RCSB PDB 6O8D · PDBe 6O8D · UniProt P10747

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