6A9K | pdb_00006a9k

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

• PDB DOI: https://doi.org/10.2210/pdb6A9K/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2018-07-13 Released: 2019-07-24 
• Deposition Author(s): Tsuchiya, Y., Fujii, I., Tada, T., Yamaguchi, A., Tsumuraya, T., Kumon, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.249 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Starting Model: experimental

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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 97.51 kDa 
• Atom Count: 7,157 
• Modeled Residue Count: 878 
• Deposited Residue Count: 878 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN 9C10 L CHAIN	A [auth L], C [auth A]	219	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
IMMUNOGLOBULIN 9C10 H CHAIN	B [auth H], D [auth B]	220	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9T0	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 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.986	α = 90
b = 36.553	β = 91.5
c = 111.986	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-07-24 
Deposition Author(s): Tsuchiya, Y., Fujii, I., Tada, T., Yamaguchi, A., Tsumuraya, T., Kumon, A.

Revision History  

• Version 1.0: 2019-07-24
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary