Research workbench
Crystal structure of ipilimumab Fab complexed with ctla-4 at 2.6A resolution
Analyse Crystal structure of ipilimumab Fab complexed with ctla-4 at 2.6A resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RP8
- Type
- protein
- Length
- 1,073 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody ipilimumab heavy chain; Antibody ipilimumab light chain; Cytotoxic T-lymphocyte…
- UniProt
- P16410
- Pockets
- 13 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| h | Antibody ipilimumab heavy chain | protein | 211 | 7% helix, 52% strand | — |
| l, L | Antibody ipilimumab light chain | protein | 212 | 7% helix, 53% strand | — |
| H | Antibody ipilimumab heavy chain | protein | 212 | 7% helix, 52% strand | — |
| C | Cytotoxic T-lymphocyte protein 4 | protein | 116 | 3% helix, 62% strand | P16410 |
| c | Cytotoxic T-lymphocyte protein 4 | protein | 110 | 0% helix, 61% strand | P16410 |
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.64 | 0.77 | 53 | empty |
| 2 | 507 | 0.64 | 0.76 | 73 | empty |
| 3 | 348 | 0.61 | 0.78 | 44 | empty |
| 4 | 339 | 0.58 | 0.77 | 50 | empty |
| 5 | 229 | 0.56 | 0.78 | 30 | empty |
Interfaces
9 interfaces between chains.
- H–L · 1635 Ų buried · 14 hydrogen bonds · protein-protein
- h–l · 1633 Ų buried · 12 hydrogen bonds · protein-protein
- h–c · 617 Ų buried · 5 hydrogen bonds · protein-protein
- H–C · 599 Ų buried · 5 hydrogen bonds · protein-protein
- l–L · 581 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6RP8 · Crystal Structure of Ipilimumab Fab complexed with CTLA-4 at 2.6A resolution · the same entry in another collection · chain c against c, 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 c 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 6RP8 · PDBe 6RP8 · UniProt P16410
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