Macromolecule Content

Total Structure Weight: 120.33 kDa
Atom Count: 7851
Modelled Residue Count: 1043
Deposited Residue Count: 1100
Unique protein chains: 3

5JXE

Human PD-1 ectodomain complexed with Pembrolizumab Fab

PDB DOI: 10.2210/pdb5JXE/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Escherichia coli, Homo sapiens
Mutation(s): Yes

Deposited: 2016-05-13 Released: 2016-08-10
Deposition Author(s): Na, Z., Bharath, S.R., Song, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.286
R-Value Work: 0.261
R-Value Observed: 0.262

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

PubMed: 27325296 Search on PubMedSearch on PubMed Central
DOI: 10.1038/cr.2016.77
Primary Citation of Related Structures:
5JXE

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Programmed cell death protein 1	A, B	114	Homo sapiens	Mutation(s): 1 Gene Names: PDCD1, PD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15116 (Homo sapiens) Explore Q15116 Go to UniProtKB: Q15116
PHAROS: Q15116
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15116
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pembrolizumab Fab light chain	C, E [auth F]	218	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Pembrolizumab Fab heavy chain	D, F [auth G]	218	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.286
R-Value Work: 0.261
R-Value Observed: 0.262
Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.554	α = 90
b = 105.554	β = 90
c = 380.048	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2016-05-13
Released Date: 2016-08-10

Deposition Author(s):

Revision History (Full details and data files)

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

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.