6RLM

Crystal structure of AT1412dm Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of a homo-dimerization site in tetraspanin CD9 targeted by a melanoma patient-derived antibody

Neviani, V.Pos, W.Schotte, R.Wagner, K.Go, D.M.Fatmawati, C.Kedde, M.Claassen, Y.B.Kroon-Batenburg, L.Lutz, M.Verdegaal, E.M.E.van der Burg, S.H.Spits, H.Gros, P.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AT1412dm Fab (Heavy Chain)
A, C, E, G, I
A, C, E, G, I, K, M, O
227Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
AT1412dm Fab (Light Chain)
B, D, F, H, J
B, D, F, H, J, L, N, P
220Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.244 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 224.909α = 90
b = 238.594β = 90
c = 209.812γ = 90
Software Package:
Software NamePurpose
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific ResearchNetherlands024.002.009

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-12
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description