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Structure of human programmed cell death 1 ligand 1 (pd-L1) with low molecular mass inhibitor
Analyse Structure of human programmed cell death 1 ligand 1 (pd-L1) with low molecular… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J89
- Type
- protein
- Length
- 501 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Programmed cell death 1 ligand 1
- UniProt
- Q9NZQ7
- Ligands
- 6GX
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B | Programmed cell death 1 ligand 1 | protein | 125 | 17% helix, 45% strand | Q9NZQ7 |
| A | Programmed cell death 1 ligand 1 | protein | 127 | 20% helix, 42% strand | Q9NZQ7 |
| D | Programmed cell death 1 ligand 1 | protein | 124 | 13% helix, 41% strand | Q9NZQ7 |
Ligands and binding sites
- 6GX · N-{2-[({2-methoxy-6-[(2-methyl[1,1'-biphenyl]-3-yl)methoxy]pyridin-3-yl}methyl)amino]ethyl}acetamide · ligand · 2 copies · chains C, D, A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.66 | 0.87 | 31 | 6GX |
| 2 | 143 | 0.66 | 0.87 | 25 | 6GX |
| 3 | 168 | 0.53 | 0.79 | 25 | empty |
| 4 | 197 | 0.50 | 0.76 | 25 | empty |
| 5 | 79 | 0.33 | 0.74 | 20 | empty |
Interfaces
4 interfaces between chains.
- C–A · 621 Ų buried · 8 hydrogen bonds · protein-protein
- D–B · 594 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 542 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 519 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5J89 · Structure of human Programmed cell death 1 ligand 1 (PD-L1) with low molecular mass… · the same entry in another collection · chain C against C, 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 5J89 · PDBe 5J89 · UniProt Q9NZQ7
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