6A9K

Crystal structure of the complex of the hydrolytic antibody Fab 9C10 with a transition-state analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the complex of the hydrolytic antibody Fab 9C10 with a transition-state analog

Tsuchiya, Y.Fujii, I.Tada, T.Yamaguchi, A.Tsumuraya, T.Kumon, A.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IMMUNOGLOBULIN 9C10 L CHAINA [auth L],
C [auth A]
219Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IMMUNOGLOBULIN 9C10 H CHAINB [auth H],
D [auth B]
220Mus musculusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9T0
Query on 9T0

Download Ideal Coordinates CCD File 
E [auth H],
F [auth B]
5-[(2R,3R)-2-[2,2-bis(chloranyl)ethanoylamino]-3-(4-nitrophenyl)-3-[oxidanyl-[[4-[2,2,2-tris(fluoranyl)ethanoylamino]phenyl]methyl]phosphoryl]oxy-propoxy]-5-oxidanylidene-pentanoic acid
C25 H25 Cl2 F3 N3 O11 P
DNCOXYFMDXAPCJ-WIYYLYMNSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.197 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.986α = 90
b = 36.553β = 91.5
c = 111.986γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description