5WKZ | pdb_00005wkz

VH1-69 germline antibody predicted from CR6261

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Trichoplusia ni
  • Mutation(s): No 

  • Deposited: 2017-07-25 Released: 2018-08-01 
  • Deposition Author(s): Lang, S., Lee, P.S.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 
    0.232 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5WKZ

This is version 1.2 of the entry. See complete history. 

Literature

Anti-idiotypic antibody K1-18 engages VH1-69 precursor and affinity-matured, anti-stem antibodies through mimicry of the HA stem

Wilson, I.A., Lang, S., Kurosawa, Y., Ohshima, N., Ota, T., Abadejos, J., Lee, P.S., Nemazee, D.

To be published.

Macromolecule Content 

  • Total Structure Weight: 49.6 kDa 
  • Atom Count: 3,559 
  • Modeled Residue Count: 433 
  • Deposited Residue Count: 467 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Immunoglobulin heavy variable 1-69D,IgG H chainA [auth H]250Homo sapiensMutation(s): 0 
Gene Names: IGHV1-69D
UniProt & NIH Common Fund Data Resources
Find proteins for A0A0B4J2H0 (Homo sapiens)
Explore A0A0B4J2H0 
Go to UniProtKB:  A0A0B4J2H0
GTEx:  ENSG00000280411 
Find proteins for S6BAM6 (Homo sapiens)
Explore S6BAM6 
Go to UniProtKB:  S6BAM6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsA0A0B4J2H0S6BAM6
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Lambda-chain (AA -20 to 215)B [auth L]217Homo sapiensMutation(s): 0 
UniProt
Find proteins for A2NUT2 (Homo sapiens)
Explore A2NUT2 
Go to UniProtKB:  A2NUT2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2NUT2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4


Download:Ideal Coordinates CCD File
C [auth H]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free:  0.232 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.206 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.233α = 90
b = 84.233β = 90
c = 177.544γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR56 AI 117675

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-01
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.2: 2024-10-23
    Changes: Data collection, Database references, Structure summary