5GIR

Crystal structure of a Fab fragment with its ligand peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.182

Literature

Macromolecules
Sequence Display for 5GIR

Classification: IMMUNE SYSTEM

Total Structure Weight: 106973.28

Macromolecule Entities
Molecule Chains Length Organism Details
Heavy chain of Fab fragment A, H 240 Mus musculus
Light chain of Fab fragment B, L 234 Mus musculus
LYS-PRO-ILE-ILE-ILE-GLY-SER-HIS-ALA-TYR-GLY-ASP C, D 12 Homo sapiens EC#: 1.1.1.42 IUBMB
Gene Name(s): IDH1 Gene View PICD
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

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

A 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PCA
Query on PCA
A, H L-PEPTIDE LINKING C5 H7 N O3 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.182
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 69.11 α = 90.00
b = 93.65 β = 107.51
c = 70.56 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-06-24
  • Released Date: 2016-09-14
  • Deposition author(s): Kitago, Y., Kaneko, K.K., Ogasawara, S., Kato, Y., Takagi, J.

Revision History

  • Version 1_0: 2016-09-14

    Type: Initial release