› 8as0

X-ray diffraction
3.5Å resolution

PD-1 extracellular domain in complex with Fab fragment from D12 antibody

Released:
DOI: 10.2210/pdb8as0/pdb
PDB entry 8as0 coloured by chain, front view.
PDB entry 8as0 coloured by chain, side view.
PDB entry 8as0 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Selection of a PD-1 blocking antibody from a novel fully human phage display library.
Peissert F, Plüss L, Giudice AM, Ongaro T, Villa A, Elsayed A, Nadal L, Plaza SD, Scietti L, Puca E, De Luca R, Forneris F, Neri D
Protein Sci e4486 (2022)
PMID: 36317676

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-226221 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (10 distinct):
D12 antibody light chain, Fab fragment Chains: C, D, G, J, M, P, S, V
Molecule details ›
Chains: C, D, G, J, M, P, S, V
Length: 214 amino acids
Theoretical weight: 23.34 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
D12 antibody heavy chain, Fab fragment Chains: B, E, H, K, N, Q, T, W
Molecule details ›
Chains: B, E, H, K, N, Q, T, W
Length: 225 amino acids
Theoretical weight: 23.79 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
Programmed cell death protein 1 Chains: A, F, I, L, O, R, X, Y
Molecule details ›
Chains: A, F, I, L, O, R, X, Y
Length: 168 amino acids
Theoretical weight: 19.07 KDa
Source organism: Homo sapiens
Expression system: Cricetulus griseus
UniProt:
  • Canonical: Q15116 (Residues: 24-170; Coverage: 56%)
Gene names: PD1, PDCD1
Sequence domains: Immunoglobulin V-set domain

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, FUC
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN, FUC
Carbohydrate polymer
1 bound ligand:
Ligand NAG 8 x NAG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE MASSIF-1
Spacegroup: P21
Unit cell:
a: 81.195Å b: 187.092Å c: 190.845Å
α: 90° β: 90.24° γ: 90°
R-values:
R R work R free
0.246 0.243 0.293
Expression system: Cricetulus griseus

Quick links

Citations

2 citation in other articles

Adapting Neutralizing Antibodies to Viral Variants by Structure-Guided Affinity Maturation Using Phage Display Technology.
Peissert et al. (2023)
1 more

1 mention without citation

Selection of a PD-1 blocking antibody from a novel fully human phage display library.
Peissert et al. (2022)