5DK3

Crystal Structure of Pembrolizumab, a full length IgG4 antibody


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.184

Literature

Macromolecules
Sequence Display for 5DK3

Classification: IMMUNE SYSTEM

Total Structure Weight: 150169.75

Macromolecule Entities
Molecule Chains Length Organism Details
Light Chain A, F 218 Homo sapiens
Heavy Chain B, G 444 Homo sapiens

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SUC
Query on SUC

B, G SUCROSE
C12 H22 O11
CZMRCDWAGMRECN-UGDNZRGBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

B, G N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

B, G ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

B, G BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

G ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.223
  • R-Value Work: 0.184
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 63.83 α = 90.00
b = 110.83 β = 90.00
c = 264.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2015-09-02
  • Released Date: 2015-11-18
  • Deposition author(s): Scapin, G., Prosise, W., Reichert, P.

Revision History

  • Version 1_0: 2015-11-18

    Type: Initial release

  • Version 1_1: 2016-07-06

    Type: Database references

  • Version 1_2: 2016-08-03

    Type: Database references