MolNFT v1 · #187741 · protein
Crystal structure of an acidic pH-selective ipilimumab variant IPI.105 in complex with ctla-4
7SU0 · Cytotoxic T-lymphocyte protein 4: “Crystal structure of an acidic pH-selective ipilimumab variant IPI.105 in complex with ctla-4”. X-ray diffraction, 1 ligand (NAG), 12 pockets (best druggability 0.76). MolNFT v1 #187741 on…
- PDB
- 7SU0
- Type
- protein
- Length
- 1,081 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytotoxic T-lymphocyte protein 4; Fab heavy chain; Fab light chain
- UniProt
- P16410
- Ligands
- NAG
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cytotoxic T-lymphocyte protein 4 | protein | 117 | 3% helix, 56% strand | P16410 |
| H | Fab heavy chain | protein | 212 | 8% helix, 52% strand | — |
| L | Fab light chain | protein | 214 | 5% helix, 52% strand | — |
| D | Cytotoxic T-lymphocyte protein 4 | protein | 116 | 3% helix, 57% strand | P16410 |
| I | Fab heavy chain | protein | 210 | 7% helix, 53% strand | — |
| M | Fab light chain | protein | 212 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains C, D
- FLC · Citrate anion · additive · chains D, I, M
- PEG · Di(hydroxyethyl)ether · additive · chains I, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 790 | 0.76 | 0.81 | 99 | empty |
| 2 | 468 | 0.60 | 0.75 | 37 | empty |
| 3 | 270 | 0.55 | 0.77 | 28 | empty |
| 4 | 365 | 0.55 | 0.74 | 44 | PEG |
| 5 | 178 | 0.54 | 0.79 | 28 | FLC |
Interfaces
10 interfaces between chains.
- H–L · 1600 Ų buried · 6 hydrogen bonds · protein-protein
- I–M · 1590 Ų buried · 8 hydrogen bonds · protein-protein
- D–I · 630 Ų buried · 7 hydrogen bonds · protein-protein
- C–H · 590 Ų buried · 6 hydrogen bonds · protein-protein
- D–M · 400 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 3 glycan, 2 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 7SU0 · Crystal structure of an acidic pH-selective Ipilimumab variant Ipi.105 in complex with… · the same entry in another collection · chain M against M, 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 D against A, TM-score 0.97
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 7SU0 · PDBe 7SU0 · UniProt P16410
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