5CBA

3B4 in complex with CXCL13 - 3B4-CXCL13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A Combination of Structural and Empirical Analyses Delineates the Key Contacts Mediating Stability and Affinity Increases in an Optimized Biotherapeutic Single-chain Fv (scFv).

Tu, C.Terraube, V.Tam, A.S.Stochaj, W.Fennell, B.J.Lin, L.Stahl, M.LaVallie, E.R.Somers, W.Finlay, W.J.Mosyak, L.Bard, J.Cunningham, O.

(2016) J. Biol. Chem. 291: 1267-1276


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3b4 heavy chain
A, C
142N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
3b4 light chain
B, D
117N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
C-X-C motif chemokine 13
E, F
88Homo sapiensMutation(s): 0 
Gene Names: CXCL13 (BCA1, BLC, SCYB13)
Find proteins for O43927 (Homo sapiens)
Go to Gene View: CXCL13
Go to UniProtKB:  O43927
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, E
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.197 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 119.350α = 90.00
b = 55.680β = 120.56
c = 112.770γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2018-11-14
    Type: Advisory, Data collection, Database references, Derived calculations, Source and taxonomy