MolNFT v1 · #28605 · protein

Crystal structure of human CD28 in complex with the Fab fragment of a mitogenic antibody (5.11A1)

1YJD · Fab fragment of 5.11A1 antibody light chain: “Crystal structure of human CD28 in complex with the Fab fragment of a mitogenic antibody (5.11A1)”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.69). MolNFT v1…

PDB: 1YJD
Type: protein
Length: 547 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab fragment of 5.11A1 antibody light chain; Fab fragment of 5.11A1 antibody heavy chain…
UniProt: P10747
Ligands: NAG
Pockets: 7 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 4% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab fragment of 5.11A1 antibody light chain	protein	212	5% helix, 50% strand	—
H	Fab fragment of 5.11A1 antibody heavy chain	protein	217	4% helix, 52% strand	—
C	T-cell-specific surface glycoprotein CD28	protein	118	3% helix, 55% strand	P10747

Ligands and binding sites

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

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

Pockets

7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	50	0.69	0.97	16	empty
2	249	0.53	0.77	35	empty
3	228	0.47	0.74	40	empty
4	79	0.33	0.75	16	empty
5	61	0.28	0.74	17	empty

Interfaces

3 interfaces between chains.

L–H · 1953 Å² buried · 18 hydrogen bonds · protein-protein
H–C · 526 Å² buried · 9 hydrogen bonds · protein-protein
L–C · 209 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

1YJD · Crystal structure of human CD28 in complex with the Fab fragment of a mitogenic antibody… · the same entry in another collection · chain L against L, 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 0.98

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 1YJD · PDBe 1YJD · UniProt P10747

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