5JXE

Human PD-1 ectodomain complexed with Pembrolizumab Fab

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural basis for blocking PD-1-mediated immune suppression by therapeutic antibody pembrolizumab.

Na, Z., Yeo, S.P., Bharath, S.R., Bowler, M.W., Balijkcij, E., Wang, C.I., Song, H.

(2017) Cell Res. 27: 147-150


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Programmed cell death protein 1
A, B
114Homo sapiensMutation(s): 1 
Gene Names: PDCD1 (PD1)
Find proteins for Q15116 (Homo sapiens)
Go to Gene View: PDCD1
Go to UniProtKB:  Q15116
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Pembrolizumab Fab light chain
C, F
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Pembrolizumab Fab heavy chain
D, G
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.261 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 105.554α = 90.00
b = 105.554β = 90.00
c = 380.048γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-09-07
    Type: Experimental preparation
  • Version 1.2: 2017-12-06
    Type: Database references, Derived calculations