5C6W

anti-CXCL13 scFv - E10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 
    0.164 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.154 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Optimization of a scFv-based biotherapeutic by CDR side-chain clash repair

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein IGHV1-69-2,Ig lambda chain V-II region NIG-84A [auth H],
B [auth J]
264Homo sapiensMutation(s): 0 
Gene Names: IGHV1-69-2
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J2H0 (Homo sapiens)
Explore A0A0B4J2H0 
Go to UniProtKB:  A0A0B4J2H0
GTEx:  ENSG00000280411 
Find proteins for P01704 (Homo sapiens)
Explore P01704 
Go to UniProtKB:  P01704
GTEx:  ENSG00000211666 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA0A0B4J2H0P01704
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PEG
Query on PEG

Download Ideal Coordinates CCD File 
RA [auth J],
Z [auth H]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth J],
DA [auth J],
EA [auth J],
G [auth H],
H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
FA [auth J]
GA [auth J]
HA [auth J]
I [auth H]
IA [auth J]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AA [auth J]
BA [auth J]
C [auth H]
D [auth H]
E [auth H]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free:  0.164 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.154 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.98α = 90
b = 80.36β = 90
c = 119.24γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-04
    Type: Initial release
  • Version 1.1: 2017-11-01
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2023-09-27
    Changes: Data collection, Database references, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary