7YZJ | pdb_00007yzj

FAB IN COMPLEX WITH ANTIGENIC PEPTIDE OF INTERLEUKIN-2

• PDB DOI: https://doi.org/10.2210/pdb7YZJ/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Mus musculus, Homo sapiens
• Mutation(s): No 


• Deposited: 2022-02-20 Released: 2023-02-01 
• Deposition Author(s): Pletnev, V., Pletneva, N.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

Literature

Three-Dimensional Structure of Fab Fragment of Monoclonal Antibody LNKB-2 Complexed with Antigenic Nonapeptide from Human Interleukin-2

Pletnev, V., Pletneva, N., Goryacheva, E., Artemiev, I.

(2023) Russ J Bioorg Chem 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 49.11 kDa 
• Atom Count: 3,507 
• Modeled Residue Count: 448 
• Deposited Residue Count: 448 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of FAB fragment	A [auth L]	219	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of FAB fragment	B [auth H]	220	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigenic peptide	C [auth E]	9	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P60568 (Homo sapiens) Explore P60568  Go to UniProtKB:  P60568
PHAROS:  P60568 GTEx:  ENSG00000109471

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.240 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.935	α = 90
b = 72.218	β = 90
c = 88.33	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-02-01 
Deposition Author(s): Pletnev, V., Pletneva, N.

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Funding Organization	Location	Grant Number
Not funded	Russian Federation	--

Revision History  

• Version 1.0: 2023-02-01
  Type: Initial release
  
• Version 1.1: 2024-02-07
  Changes: Data collection, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary