MolNFT v1 · #105291 · protein

Anti-canine CD28 antibody, 1C6, bound canine CD28

4R0L · Antibody 1C6 heavy chain: “Anti-canine CD28 antibody, 1C6, bound canine CD28”. X-ray diffraction, 2 ligands (NAG, FUC), 7 pockets (best druggability 0.77). MolNFT v1 #105291 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 4R0L
Type: protein
Length: 686 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody 1C6 heavy chain; T-cell costimulatory molecule CD28; Antibody 1C6 light chain
UniProt: Q9N0N8
Ligands: NAG, FUC
Pockets: 7 · best druggability 0.77

Structure

x-ray diffraction · 6 distinct chains · 3% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antibody 1C6 heavy chain	protein	113	5% helix, 47% strand	—
C	T-cell costimulatory molecule CD28	protein	117	3% helix, 56% strand	Q9N0N8
D	T-cell costimulatory molecule CD28	protein	118	3% helix, 54% strand	Q9N0N8
H	Antibody 1C6 heavy chain	protein	111	5% helix, 43% strand	—
L	Antibody 1C6 light chain	protein	113	3% helix, 47% strand	—
B	Antibody 1C6 light chain	protein	114	3% helix, 46% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 11 copies · chains C, B, D, L, A, H
FUC · alpha-L-fucopyranose · sugar · 2 copies · chains C

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

Pockets

7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	343	0.77	0.87	45	empty
2	273	0.76	0.88	35	empty
3	125	0.66	0.89	33	empty
4	92	0.63	0.89	27	empty
5	89	0.40	0.77	33	empty

Interfaces

7 interfaces between chains.

A–B · 644 Å² buried · 9 hydrogen bonds · protein-protein
H–L · 643 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 506 Å² buried · 7 hydrogen bonds · protein-protein
D–H · 460 Å² buried · 8 hydrogen bonds · protein-protein
C–B · 454 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 8 glycan (disulfide, N-glycosylation).

Compared structures

4R0L · Anti-canine CD28 antibody, 1C6, bound canine CD28 · the same entry in another collection · chain A against A, TM-score 1.00

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 Q9N0N8
Elsewhere: RCSB PDB 4R0L · PDBe 4R0L · UniProt Q9N0N8

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