› 5b8c

X-ray diffraction
2.15Å resolution

High resolution structure of the human PD-1 in complex with pembrolizumab Fv

Released:
DOI: 10.2210/pdb5b8c/pdb
PDB entry 5b8c coloured by chain, front view.
PDB entry 5b8c coloured by chain, side view.
PDB entry 5b8c coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
High-resolution crystal structure of the therapeutic antibody pembrolizumab bound to the human PD-1.
Horita S, Nomura Y, Sato Y, Shimamura T, Iwata S, Nomura N
Sci Rep 6 35297 (2016)
PMID: 27734966

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-235378 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Pembrolizumab light chain variable region (PemVL) Chains: A, D, G, J
Molecule details ›
Chains: A, D, G, J
Length: 119 amino acids
Theoretical weight: 12.99 KDa
Source organism: Homo sapiens
Expression system: Brevibacillus choshinensis
Structure domains: Immunoglobulins
Pembrolizumab heavy chain variable region (PemVH) Chains: B, E, H, K
Molecule details ›
Chains: B, E, H, K
Length: 120 amino acids
Theoretical weight: 13.49 KDa
Source organism: Homo sapiens
Expression system: Brevibacillus choshinensis
Structure domains: Immunoglobulins
Programmed cell death protein 1 Chains: C, F, I, L
Molecule details ›
Chains: C, F, I, L
Length: 139 amino acids
Theoretical weight: 15.51 KDa
Source organism: Homo sapiens
Expression system: Brevibacillus choshinensis
UniProt:
  • Canonical: Q15116 (Residues: 32-160; Coverage: 49%)
Gene names: PD1, PDCD1
Sequence domains: Immunoglobulin V-set domain
Structure domains: Immunoglobulins

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 143.68Å b: 143.13Å c: 76.55Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.184 0.226
Expression system: Brevibacillus choshinensis

Quick links

Citations

6 review citations

Structural Biology of the Immune Checkpoint Receptor PD-1 and Its Ligands PD-L1/PD-L2.
Zak et al. (2017)
5 more

13 mentions without citation

Molecular Interactions of Antibody Drugs Targeting PD-1, PD-L1, and CTLA-4 in Immuno-Oncology.
Lee et al. (2019)
12 more