MolNFT v1 · #123234 · protein
Crystal structure of pd-L1 complexed with a nanobody at 1.7 angstron resolution
5JDS: “Crystal structure of pd-L1 complexed with a nanobody at 1.7 angstron resolution”. X-ray diffraction, 3 ligands (NA, CL, SO4), 1 pocket (best druggability 0.33). MolNFT v1 #123234 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5JDS
- Type
- protein
- Length
- 242 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nanobody; Programmed cell death 1 ligand 1
- UniProt
- Q9NZQ7
- Ligands
- NA, CL, SO4
- Pockets
- 1 · best druggability 0.33
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Nanobody | protein | 127 | 11% helix, 46% strand | — |
| A | Programmed cell death 1 ligand 1 | protein | 115 | 8% helix, 48% strand | Q9NZQ7 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains B, A
- CL · Chloride ion · ion · 3 copies · chains B
- SO4 · Sulfate ion · ion · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.33 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- B–A · 676 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5JDS · Crystal structure of PD-L1 complexed with a nanobody at 1.7 Angstron resolution · the same entry in another collection · chain B against B, 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 5JDS · PDBe 5JDS · UniProt Q9NZQ7
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