Research workbench
Complex structure of ipilimumab-scfv and ctla-4
Analyse Complex structure of ipilimumab-scfv and ctla-4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XJ3
- Type
- protein
- Length
- 1,360 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ipilimumab-vh; Ipilimumab-vl; Cytotoxic T-lymphocyte protein 4
- UniProt
- P16410
- Pockets
- 17 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Ipilimumab-vh | protein | 117 | 5% helix, 51% strand | — |
| B, E, H, K | Ipilimumab-vl | protein | 108 | 3% helix, 51% strand | — |
| C, F, I, L | Cytotoxic T-lymphocyte protein 4 | protein | 115 | 3% helix, 50% strand | P16410 |
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 551 | 0.70 | 0.79 | 71 | empty |
| 2 | 432 | 0.69 | 0.81 | 61 | empty |
| 3 | 479 | 0.66 | 0.78 | 36 | empty |
| 4 | 355 | 0.65 | 0.79 | 34 | empty |
| 5 | 412 | 0.63 | 0.78 | 46 | empty |
Interfaces
26 interfaces between chains.
- D–E · 762 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 755 Ų buried · 6 hydrogen bonds · protein-protein
- J–K · 751 Ų buried · 6 hydrogen bonds · protein-protein
- G–H · 750 Ų buried · 5 hydrogen bonds · protein-protein
- G–I · 606 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 5XJ3 · Complex structure of ipilimumab-scFv and CTLA-4 · the same entry in another collection · chain K against K, 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 P16410
- Elsewhere: RCSB PDB 5XJ3 · PDBe 5XJ3 · UniProt P16410
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