Research workbench
Anti-canine CD28 antibody, 1C6, bound canine CD28
Analyse Anti-canine CD28 antibody, 1C6, bound canine CD28 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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.
| Volume (ų) | 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 Ų buried · 9 hydrogen bonds · protein-protein
- H–L · 643 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 506 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 460 Ų buried · 8 hydrogen bonds · protein-protein
- C–B · 454 Ų 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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