MolNFT v1 · #158176 · protein
Pd-L1 igv domain bound to fragment
6NM7 · Programmed cell death 1 ligand 1: “Pd-L1 igv domain bound to fragment”. X-ray diffraction, 1 ligand (22L), 2 pockets (best druggability 0.69). MolNFT v1 #158176 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6NM7
- Type
- protein
- Length
- 252 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death 1 ligand 1
- UniProt
- Q9NZQ7
- Ligands
- 22L
- Pockets
- 2 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 16% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Programmed cell death 1 ligand 1 | protein | 126 | 16% helix, 40% strand | Q9NZQ7 |
Ligands and binding sites
- 22L · 5-phenylthieno[2,3-d]pyrimidin-4(3H)-one · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.69 | 0.90 | 22 | 22L |
| 2 | 65 | 0.28 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 584 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6NM7 · PD-L1 IgV domain bound to fragment · the same entry in another collection · chain A against A, 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 Q9NZQ7
- Elsewhere: RCSB PDB 6NM7 · PDBe 6NM7 · UniProt Q9NZQ7
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