5YOY

Crystal structure of the human tumor necrosis factor in complex with golimumab Fv


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.727 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for tumor necrosis factor blockade with the therapeutic antibody golimumab

Ono, M.Horita, S.Sato, Y.Nomura, Y.Iwata, S.Nomura, N.

(2018) Protein Sci. 27: 1038-1046


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tumor necrosis factor
A, B, C, J, K, L
173Homo sapiensMutation(s): 0 
Gene Names: TNF (TNFA, TNFSF2)
Find proteins for P01375 (Homo sapiens)
Go to Gene View: TNF
Go to UniProtKB:  P01375
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Golimumab light chain variable region
D, E, F, M, N, O
119N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Golimumab heavy chain variable region
G, H, I, P, Q, R
129N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.727 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.190 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 133.640α = 90.00
b = 85.300β = 101.61
c = 135.960γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Science and TechnologyJapan--
Japan Society for the Promotion of ScienceJapan15K06968
Japan Society for the Promotion of ScienceJapan15J04343
Japan Agency of Medical Research and DevelopmentJapan--

Revision History 

  • Version 1.0: 2018-05-09
    Type: Initial release
  • Version 1.1: 2018-06-20
    Type: Data collection, Database references
  • Version 1.2: 2018-11-14
    Type: Data collection, Derived calculations