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- PDB-2hrp: ANTIGEN-ANTIBODY COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2hrp
TitleANTIGEN-ANTIBODY COMPLEX
Components
  • (MONOCLONAL ANTIBODY F11.2.32) x 2
  • HIV-1 PROTEASE PEPTIDE
KeywordsCOMPLEX (IMMUNOGLOBULIN/PEPTIDE) / FAB FRAGMENT / CROSS-REACTIVITY / HIV1 PROTEASE / ENZYME INHIBITION / COMPLEX (IMMUNOGLOBULIN-PEPTIDE) / COMPLEX (IMMUNOGLOBULIN-PEPTIDE) complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLescar, J. / Bentley, G.A.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Three-dimensional structure of an Fab-peptide complex: structural basis of HIV-1 protease inhibition by a monoclonal antibody.
Authors: Lescar, J. / Stouracova, R. / Riottot, M.M. / Chitarra, V. / Brynda, J. / Fabry, M. / Horejsi, M. / Sedlacek, J. / Bentley, G.A.
#1: Journal: Protein Sci. / Year: 1996
Title: Preliminary Crystallographic Studies of an Anti-HIV-1 Protease Antibody that Inhibits Enzyme Activity
Authors: Lescar, J. / Stouracova, R. / Riottot, M.M. / Chitarra, V. / Brynda, J. / Fabry, M. / Horejsi, M. / Sedlacek, J. / Bentley, G.A.
History
DepositionDec 27, 1996Processing site: BNL
Revision 1.0Dec 31, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: MONOCLONAL ANTIBODY F11.2.32
H: MONOCLONAL ANTIBODY F11.2.32
P: HIV-1 PROTEASE PEPTIDE
M: MONOCLONAL ANTIBODY F11.2.32
N: MONOCLONAL ANTIBODY F11.2.32
Q: HIV-1 PROTEASE PEPTIDE


Theoretical massNumber of molelcules
Total (without water)99,0416
Polymers99,0416
Non-polymers00
Water7,134396
1
L: MONOCLONAL ANTIBODY F11.2.32
H: MONOCLONAL ANTIBODY F11.2.32
P: HIV-1 PROTEASE PEPTIDE


Theoretical massNumber of molelcules
Total (without water)49,5203
Polymers49,5203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-33 kcal/mol
Surface area19930 Å2
MethodPISA
2
M: MONOCLONAL ANTIBODY F11.2.32
N: MONOCLONAL ANTIBODY F11.2.32
Q: HIV-1 PROTEASE PEPTIDE


Theoretical massNumber of molelcules
Total (without water)49,5203
Polymers49,5203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-33 kcal/mol
Surface area19430 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12380 Å2
ΔGint-77 kcal/mol
Surface area36800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.300, 96.310, 105.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99997, -0.00218, -0.00742), (0.00238, -0.99962, -0.02728), (-0.00736, -0.0273, 0.9996)39.34, 1.14, 0.34
2given(-0.99997, -0.00218, -0.00742), (0.00238, -0.99962, -0.02728), (-0.00736, -0.0273, 0.9996)39.34, 1.14, 0.34
3given(-0.99997, -0.00218, -0.00742), (0.00238, -0.99962, -0.02728), (-0.00736, -0.0273, 0.9996)39.34, 1.14, 0.34

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Components

#1: Antibody MONOCLONAL ANTIBODY F11.2.32 / IMMUNOGLOBULIN / IGG1


Mass: 23981.467 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / Strain: BALB/C / References: GenBank: 600718
#2: Antibody MONOCLONAL ANTIBODY F11.2.32 / IMMUNOGLOBULIN / IGG1


Mass: 24336.324 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / Strain: BALB/C / References: GenBank: 600716
#3: Protein/peptide HIV-1 PROTEASE PEPTIDE


Mass: 1202.491 Da / Num. of mol.: 2 / Fragment: RESIDUES 36 - 46
Source method: isolated from a genetically manipulated source
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.25 mg/mlFab F11.2.321drop
21.25 mg/mlpeptide1drop
322 %PEG20001reservoir
40.04 %1reservoirNaN3
50.1 MTris-HCl1reservoir
62 %(v/v)glycerol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 3, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 49323 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.5 / Rsym value: 0.48 / % possible all: 98.7
Reflection shell
*PLUS
% possible obs: 98.7 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FBI

1fbi


Resolution: 2.2→7 Å / Rfactor Rfree error: 0.03 / Data cutoff high absF: 100000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.289 333 5 %RANDOM
Rwork0.198 ---
obs0.198 3517 97 %-
Displacement parametersBiso mean: 20.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.25 Å
Luzzati d res low-7 Å
Luzzati sigma a0.25 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6852 0 0 396 7248
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.73
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.14
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.58
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.381.5
X-RAY DIFFRACTIONx_mcangle_it22
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it2.52.5
LS refinement shellResolution: 2.2→2.3 Å / Rfactor Rfree error: 0.05 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.315 50 5 %
Rwork0.25 3371 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 35173 / Rfactor all: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.14
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.58
LS refinement shell
*PLUS
Rfactor obs: 0.25

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