› 5jds

X-ray diffraction
1.7Å resolution

Crystal structure of PD-L1 complexed with a nanobody at 1.7 Angstron resolution

Released:
DOI: 10.2210/pdb5jds/pdb
PDB entry 5jds coloured by chain, front view.
PDB entry 5jds coloured by chain, side view.
PDB entry 5jds coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of a novel PD-L1 nanobody for immune checkpoint blockade.
Zhang F, Wei H, Wang X, Bai Y, Wang P, Wu J, Jiang X, Wang Y, Cai H, Xu T, Zhou A
Cell Discov 3 17004 (2017)
PMID: 28280600

Function and Biology Details

Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212800 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Nanobody Chain: B
Molecule details ›
Chain: B
Length: 146 amino acids
Theoretical weight: 15.77 KDa
Source organism: Camelidae
Expression system: Homo sapiens
Structure domains: Immunoglobulins
Programmed cell death 1 ligand 1 Chain: A
Molecule details ›
Chain: A
Length: 124 amino acids
Theoretical weight: 14.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NZQ7 (Residues: 18-132; Coverage: 42%)
Gene names: B7H1, CD274, PDCD1L1, PDCD1LG1, PDL1
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins

Ligands and Environments

3 bound ligands:
Ligand NA 2 x NA
Ligand CL 3 x CL
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P61
Unit cell:
a: 83.13Å b: 83.13Å c: 73.23Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.18 0.178 0.204
Expression systems:
  • Homo sapiens
  • Escherichia coli

Quick links

Citations

27 review citations

Nanobodies and Nanobody-Based Human Heavy Chain Antibodies As Antitumor Therapeutics.
Bannas et al. (2017)
26 more

13 mentions without citation

Structure and development of single domain antibodies as modules for therapeutics and diagnostics.
Hoey et al. (2019)
12 more