1CFN

ANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH AN EPITOPE-RELATED PEPTIDE

• PDB DOI: https://doi.org/10.2210/pdb1CFN/pdb

• Classification: POLYSPECIFICITY
• Organism(s): Mus musculus, synthetic construct
• Mutation(s): No 


• Deposited: 1999-03-19 Released: 1999-03-30 
• Deposition Author(s): Keitel, T., Kramer, A., Wessner, H., Scholz, C., Schneider-Mergener, J., Hoehne, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.325 
• R-Value Work: 0.277 

Literature

Crystallographic analysis of anti-p24 (HIV-1) monoclonal antibody cross-reactivity and polyspecificity.

Keitel, T., Kramer, A., Wessner, H., Scholz, C., Schneider-Mergener, J., Hohne, W.

(1997) Cell 91: 811-820

• PubMed: 9413990 
• DOI: https://doi.org/10.1016/s0092-8674(00)80469-9
• Primary Citation of Related Structures:  
  1BOG, 1CFN, 1CFQ, 1CFS, 1CFT, 1HI6


• PubMed Abstract: 
  

  The X-ray crystal structures of an anti-p24 (HIV-1) monoclonal antibody Fab fragment alone and in complexes with the epitope peptide GATPQDLNTnL (n = norleucine), an epitope-homologous peptide GATPEDLNQKLAGN, as well as two unrelated peptides GLYEWGGARITNTD and efslkGpllqwrsG (D-peptide), are presented to a maximum resolution of 2.6 A. The latter three peptides were identified from screening synthetic combinatorial peptide libraries. Although all peptides bind to the same antigen combining site, the nonhomologous peptides adopt different binding conformations and also form their critical contacts with different antibody residues. Only small readjustments are observed within the framework of the Fab fragment upon binding.

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Organizational Affiliation: 

Institut für Biochemie, Universitätsklinikum Charité, Humboldt-Universität zu Berlin, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Macromolecule Content

• Total Structure Weight: 47.63 kDa 
• Atom Count: 3,369 
• Modelled Residue Count: 437 
• Deposited Residue Count: 437 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (IGG2A KAPPA ANTIBODY CB41 (LIGHT CHAIN))	A	214	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01837 (Mus musculus) Explore P01837  Go to UniProtKB:  P01837

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (IGG2A-KAPPA ANTIBODY CB41 (HEAVY CHAIN))	B	213	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01864 (Mus musculus) Explore P01864  Go to UniProtKB:  P01864

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (BOUND PEPTIDE)	C	10	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NLE	C	L-PEPTIDE LINKING	C6 H13 N O2		LEU

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 0.325 
• R-Value Work: 0.277 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 105.44	α = 90
b = 105.44	β = 90
c = 295.79	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
CCP4	data reduction
AMoRE	phasing
CCP4	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-03-30 
Deposition Author(s): Keitel, T., Kramer, A., Wessner, H., Scholz, C., Schneider-Mergener, J., Hoehne, W.

Revision History  

• Version 1.0: 1999-03-30
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-06-24
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy
• Version 1.4: 2023-08-09
  Changes: Data collection, Database references, Refinement description
• Version 1.5: 2023-11-15
  Changes: Data collection