MolNFT v1 · #123067 · protein
Structure of human programmed cell death 1 ligand 1 (pd-L1) with low molecular mass inhibitor
5J8O: “Structure of human programmed cell death 1 ligand 1 (pd-L1) with low molecular mass inhibitor”. X-ray diffraction, 1 ligand (6GZ), 2 pockets (best druggability 0.63). MolNFT v1 #123067 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5J8O
- Type
- protein
- Length
- 246 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
- 6GZ
- Pockets
- 2 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Programmed cell death 1 ligand 1 | protein | 122 | 13% helix, 43% strand | Q9NZQ7 |
| B | Programmed cell death 1 ligand 1 | protein | 124 | 15% helix, 42% strand | Q9NZQ7 |
Ligands and binding sites
- 6GZ · (2R)-1-({3-bromo-4-[(2-methyl[1,1'-biphenyl]-3-yl)methoxy]phenyl}methyl)piperidine-2-carboxylic acid · 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 | 185 | 0.63 | 0.83 | 28 | 6GZ |
| 2 | 85 | 0.33 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 533 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5J8O · Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass… · 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 5J8O · PDBe 5J8O · UniProt Q9NZQ7
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