5X5X

Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219

  • Classification: IMMUNE SYSTEM
  • Expression System: Escherichia coli

  • Deposited: 2017-02-18 Released: 2018-02-21 
  • Deposition Author(s): Komatsu, M., Dong, J., Ueda, H., Arai, R.
  • Funding Organization(s): Cooperative Research Program of Network Joint Research Center for Materials and Devices; Japan Society for the Promotion of Science 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219

Arai, R.Komatsu, M.Dong, J.Ueda, H.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fd chain of anti-osteocalcin antibody KTM219
H
249N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
L chain of anti-osteocalcin antibody KTM219
L
232N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
H, L
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
H
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE

Download SDF File 
Download CCD File 
L
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download SDF File 
Download CCD File 
H
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 
  • Space Group: P 21 2 21
Unit Cell:
Length (Å)Angle (°)
a = 64.800α = 90.00
b = 71.472β = 90.00
c = 96.882γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
DENZOdata reduction
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cooperative Research Program of Network Joint Research Center for Materials and DevicesJapan20161175
Japan Society for the Promotion of ScienceJapanJP15H04191
Japan Society for the Promotion of ScienceJapanJP24780097
Japan Society for the Promotion of ScienceJapanJP16H00761
Japan Society for the Promotion of ScienceJapanJP16K05841
Japan Society for the Promotion of ScienceJapanJP26420793
Japan Society for the Promotion of ScienceJapanJP24360336

Revision History 

  • Version 1.0: 2018-02-21
    Type: Initial release