1CFN | pdb_00001cfn

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free:
0.325 (Depositor)
R-Value Work:
0.277 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/s0092-8674(00)80469-9
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01837
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01864
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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 Query on 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 (Depositor)
R-Value Work: 0.277 (Depositor)

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

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 1999-03-30

Deposition Author(s):

Schneider-Mergener, J.

Hoehne, W.

Revision History (Full details and data files)

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
Version 1.6: 2024-10-30
Changes: Structure summary