MolNFT v1 · #162992 · protein
A non-blocking anti-ctla-4 nanobody complexed with ctla-4
6RPJ · Cytotoxic T-lymphocyte protein 4: “A non-blocking anti-ctla-4 nanobody complexed with ctla-4”. X-ray diffraction, 3 ligands (NAG, FUC, NA), 4 pockets (best druggability 0.69). MolNFT v1 #162992 on GenesisL1: 3D structure, binding…
- PDB
- 6RPJ
- Type
- protein
- Length
- 973 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytotoxic T-lymphocyte protein 4; A non-blocking ctla-4 nanobody
- UniProt
- P16410
- Ligands
- NAG, FUC, NA
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Cytotoxic T-lymphocyte protein 4 | protein | 118 | 3% helix, 54% strand | P16410 |
| B, D, F, H | A non-blocking ctla-4 nanobody | protein | 125 | 7% helix, 48% strand | — |
| E | Cytotoxic T-lymphocyte protein 4 | protein | 119 | 3% helix, 53% strand | P16410 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, E, G, C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, E, G
- NA · Sodium ion · metal · 2 copies · chains C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 651 | 0.69 | 0.77 | 51 | NA |
| 2 | 59 | 0.39 | 0.80 | 15 | empty |
| 3 | 67 | 0.35 | 0.77 | 18 | empty |
| 4 | 51 | 0.34 | 0.79 | 16 | empty |
Interfaces
9 interfaces between chains.
- G–H · 808 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 807 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 793 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 792 Ų buried · 24 hydrogen bonds · protein-protein
- C–E · 651 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 6RPJ · A Non-blocking anti-CTLA-4 Nanobody complexed with CTLA-4 · the same entry in another collection · chain H against H, 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 0.96
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 6RPJ · PDBe 6RPJ · UniProt P16410
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