Research workbench
Crystal structure of ctla-4 complexed with the Fab of HL32 antibody
Analyse Crystal structure of ctla-4 complexed with the Fab of HL32 antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XY2
- Type
- protein
- Length
- 553 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytotoxic T-lymphocyte protein 4; Heavy chain; Light chain
- UniProt
- P16410
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytotoxic T-lymphocyte protein 4 | protein | 117 | 3% helix, 56% strand | P16410 |
| H | Heavy chain | protein | 224 | 1% helix, 50% strand | — |
| L | Light chain | protein | 212 | 6% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 629 | 0.65 | 0.75 | 59 | empty |
| 2 | 85 | 0.62 | 0.90 | 19 | empty |
| 3 | 113 | 0.36 | 0.74 | 22 | empty |
| 4 | 62 | 0.35 | 0.78 | 17 | empty |
| 5 | 57 | 0.29 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1908 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 519 Ų buried · 5 hydrogen bonds · protein-protein
- A–L · 304 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6XY2 · Crystal structure of CTLA-4 complexed with the Fab of HL32 antibody · the same entry in another collection · chain A against A, TM-score 1.00
- P16410 · AlphaFold monomer V2.0 prediction for cytotoxic T-lymphocyte protein 4 (P16410) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P16410
- Elsewhere: RCSB PDB 6XY2 · PDBe 6XY2 · UniProt P16410
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