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- PDB-1hh6: ANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH A PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1hh6
TitleANTI-P24 (HIV-1) FAB FRAGMENT CB41 COMPLEXED WITH A PEPTIDE
Components
  • IGG2A KAPPA ANTIBODY CB41 (HEAVY CHAIN)
  • IGG2A KAPPA ANTIBODY CB41 (LIGHT CHAIN)
  • PEP-4
KeywordsIMMUNE SYSTEM / ANTIBODY/PEPTIDE / POLYSPECIFICITY / CROSSREACTIVITY / FAB-FRAGMENT / HIV-1
Function / homology
Function and homology information


immunoglobulin receptor binding / immunoglobulin complex, circulating / complement activation, classical pathway / antigen binding / B cell differentiation / antibacterial humoral response / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Ig gamma-2A chain C region secreted form
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHahn, M. / Wessner, H. / Schneider-Mergener, J. / Hohne, W.
Citation
Journal: Embo J. / Year: 2000
Title: Evolutionary Transition Pathways for Changing Peptide Ligand Specificity and Structure
Authors: Hoffmuller, U. / Knaute, T. / Hahn, M. / Hohne, W. / Schneider-Mergener, J. / Kramer, A.
#1: Journal: Cell(Cambridge,Mass.) / Year: 1997
Title: Crystallographic Analysis of Anti-P24 (HIV-1) Monoclonal Antibody Cross-Reactivity and Polyspecificity
Authors: Keitel, T. / Kramer, A. / Wessner, H. / Scholz, C. / Schneider-Mergener, J. / Hohne, W.
History
DepositionDec 21, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 9, 2019Group: Data collection / Other / Source and taxonomy / Category: pdbx_database_status / pdbx_entity_src_syn / Item: _pdbx_database_status.status_code_sf
Revision 1.6Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IGG2A KAPPA ANTIBODY CB41 (LIGHT CHAIN)
B: IGG2A KAPPA ANTIBODY CB41 (HEAVY CHAIN)
C: PEP-4


Theoretical massNumber of molelcules
Total (without water)47,7563
Polymers47,7563
Non-polymers00
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4800 Å2
ΔGint-35.06 kcal/mol
Surface area19660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.960, 102.960, 294.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Antibody IGG2A KAPPA ANTIBODY CB41 (LIGHT CHAIN)


Mass: 23928.721 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: CB 4/1/1/F6 B-CELL HYBRIDOMA / Strain: BALB/C / References: UniProt: P01837*PLUS
#2: Antibody IGG2A KAPPA ANTIBODY CB41 (HEAVY CHAIN)


Mass: 22669.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: CB 4/1/1/F6 B-CELL HYBRIDOMA / Strain: BALB/C / References: UniProt: P01864*PLUS
#3: Protein/peptide PEP-4


Mass: 1158.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: EPITOPE-RELATED PEPTIDE / Source: (synth.) synthetic construct (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE IS RELATED TO THE ENTRY 1BOG. THE TWO RESIDUES IN THIS ENTRY VALB168, VALB171 ARE ...THE SEQUENCE IS RELATED TO THE ENTRY 1BOG. THE TWO RESIDUES IN THIS ENTRY VALB168, VALB171 ARE LEU168 AND LEU171 RESPECTIVELY IN THE ENTRY 1BOG

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.7 Å3/Da / Density % sol: 71 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: HANGING DROP SET UP AT ROOM TEMPERATURE, PROTEIN CONCENTRATION: 10 MG/ML, RESERVOIR: 1.8 M AMMONIUM SULFATE, 0.1 M MOPS-BUFFER, PH 7.5.
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21.8 Mammonium sulfate1reservoir
30.1 MMOPS1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→25 Å / Num. obs: 36923 / % possible obs: 99.5 % / Redundancy: 5.9 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 17.5
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.312 / Mean I/σ(I) obs: 5.4 / % possible all: 99.4

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BOG

1bog


Resolution: 2.6→25 Å / SU B: 9.6 / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.39
RfactorNum. reflection% reflectionSelection details
Rfree0.338 1499 5 %RANDOM
Rwork0.294 ---
obs-29358 99.5 %-
Refinement stepCycle: LAST / Resolution: 2.6→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3353 0 0 101 3454
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.32
X-RAY DIFFRACTIONp_mcangle_it2.32
X-RAY DIFFRACTIONp_scbond_it1.32.5
X-RAY DIFFRACTIONp_scangle_it2.12.5
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd00.3
X-RAY DIFFRACTIONp_multtor_nbd0.3710.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.57
X-RAY DIFFRACTIONp_staggered_tor2215
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor16.520
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 25 Å / Rfactor obs: 0.294
Solvent computation
*PLUS
Displacement parameters
*PLUS

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