MolNFT v1 · #154127 · protein
Study of the interactions of a novel monoclonal antibody, MAB059C, with the hpd-1 receptor
6K0Y · Antibody heavy chain: “Study of the interactions of a novel monoclonal antibody, MAB059C, with the hpd-1 receptor”. X-ray diffraction, 8 pockets (best druggability 0.56). MolNFT v1 #154127 on GenesisL1: 3D structure, binding sites…
- PDB
- 6K0Y
- Type
- protein
- Length
- 547 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antibody heavy chain; Antibody light chain; Programmed cell death protein 1
- UniProt
- Q15116
- Pockets
- 8 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antibody heavy chain | protein | 218 | 8% helix, 50% strand | — |
| B | Antibody light chain | protein | 213 | 6% helix, 51% strand | — |
| C | Programmed cell death protein 1 | protein | 116 | 5% helix, 52% strand | Q15116 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 383 | 0.56 | 0.74 | 49 | empty |
| 2 | 142 | 0.45 | 0.76 | 19 | empty |
| 3 | 164 | 0.43 | 0.74 | 31 | EDO |
| 4 | 58 | 0.40 | 0.81 | 19 | empty |
| 5 | 123 | 0.36 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1931 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 567 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 235 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6K0Y · Study of the interactions of a novel monoclonal antibody, mAb059c, with the hPD-1 receptor · the same entry in another collection · chain A against A, TM-score 1.00
- Q15116 · AlphaFold monomer V2.0 prediction for programmed cell death protein 1 (Q15116) · a predicted model of the same protein · chain C against A, TM-score 0.92
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 Q15116
- Elsewhere: RCSB PDB 6K0Y · PDBe 6K0Y · UniProt Q15116
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.