8B50

Crystal structure of a Fab fragment in complex with L-hydroxycoumarylalanine

• PDB DOI: https://doi.org/10.2210/pdb8B50/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-09-21 Released: 2023-10-04 
• Deposition Author(s): Meining, W., Eichinger, A., Skerra, A.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.221 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 

Literature

Preparation and characterization of monoclonal antibodies against a non natural amino acid carrying the 7-hydroxycoumarin side chain

Rubini, M., Meining, W., Eichinger, A., Mueller, M., Kramer, K., Skerra, 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 Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 48.88 kDa 
• Atom Count: 3,645 
• Modelled Residue Count: 434 
• Deposited Residue Count: 446 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment K12F9-22 - heavy chain	A [auth H]	227	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab fragment K12F9-22 - light chain	B [auth L]	219	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P0M (Subject of Investigation/LOI)	C [auth H]	(2~{S})-2-azanyl-3-(7-oxidanyl-2-oxidanylidene-chromen-4-yl)propanoic acid C12 H11 N O5 UURZOUPNUFWGBS-VIFPVBQESA-N
GOL (Subject of Investigation/LOI)	D [auth L]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 0.221 
• R-Value Work: 0.191 
• R-Value Observed: 0.192 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.914	α = 90
b = 70.914	β = 90
c = 91.043	γ = 120

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
BALBES	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-04 
Deposition Author(s): Meining, W., Eichinger, A., Skerra, A.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2023-10-04
  Type: Initial release