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- PDB-1kn2: CATALYTIC ANTIBODY D2.3 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1kn2
TitleCATALYTIC ANTIBODY D2.3 COMPLEX
Components
  • IG ANTIBODY D2.3 (HEAVY CHAIN)
  • IG ANTIBODY D2.3 (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / ABZYME / TRANSITION STATE ANALOG
Function / homology
Function and homology information


immunoglobulin receptor binding / metal ion binding
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
PARA-NITROPHENYL PHOSPHONOBUTANOYL L-ALANINE / Ig gamma-2A chain C region, A allele / Igk protein / :
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGigant, B. / Knossow, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2002
Title: Remarkable remote chiral recognition in a reaction mediated by a catalytic antibody.
Authors: D'Souza, L.J. / Gigant, B. / Knossow, M. / Green, B.S.
History
DepositionDec 18, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN PNE IS PARA-NITROPHENYL PHOSPHONOBUTANOYL L-ALANINE (NO2-C6H5-O-PO2-CH2-CH2-CH2-CO-NH-CH(CH3)-COOH)
Remark 999SEQUENCE THE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS. (RESIDUES H106 - H223) AND OF ...SEQUENCE THE SEQUENCES OF THE CONSTANT DOMAINS OF THE HEAVY CHAINS. (RESIDUES H106 - H223) AND OF THE LIGHT CHAINS (RESIDUES L107 - L214) HAVE NOT BEEN DETERMINED FOR THIS IMMUNOGLOBULIN. THEY HAVE BEEN ASSIGNED THE CONSENSUS SEQUENCE FOR THE CONSTANT DOMAIN OF MOUSE KAPPA LIGHT CHAIN AND FOR THE FIRST CONSTANT DOMAIN OF MOUSE GROUP 2A HEAVY CHAINS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IG ANTIBODY D2.3 (LIGHT CHAIN)
H: IG ANTIBODY D2.3 (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,02710
Polymers48,2092
Non-polymers8188
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-143 kcal/mol
Surface area19280 Å2
MethodPISA
2
L: IG ANTIBODY D2.3 (LIGHT CHAIN)
H: IG ANTIBODY D2.3 (HEAVY CHAIN)
hetero molecules

L: IG ANTIBODY D2.3 (LIGHT CHAIN)
H: IG ANTIBODY D2.3 (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,05420
Polymers96,4184
Non-polymers1,63616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area11280 Å2
ΔGint-348 kcal/mol
Surface area38440 Å2
MethodPISA
3
L: IG ANTIBODY D2.3 (LIGHT CHAIN)
hetero molecules

L: IG ANTIBODY D2.3 (LIGHT CHAIN)
hetero molecules

H: IG ANTIBODY D2.3 (HEAVY CHAIN)

H: IG ANTIBODY D2.3 (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)98,05420
Polymers96,4184
Non-polymers1,63616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
crystal symmetry operation2_665-y+1,x-y+1,z+1/31
crystal symmetry operation5_665x-y+1,-y+1,-z+2/31
Buried area4430 Å2
ΔGint-384 kcal/mol
Surface area45290 Å2
MethodPISA
4
L: IG ANTIBODY D2.3 (LIGHT CHAIN)
hetero molecules

H: IG ANTIBODY D2.3 (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)49,02710
Polymers48,2092
Non-polymers8188
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_665x-y+1,-y+1,-z+2/31
Buried area1910 Å2
ΔGint-160 kcal/mol
Surface area22850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.275, 78.275, 158.952
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody IG ANTIBODY D2.3 (LIGHT CHAIN)


Mass: 24019.842 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q8K0F8, UniProt: Q58EU8*PLUS
#2: Antibody IG ANTIBODY D2.3 (HEAVY CHAIN)


Mass: 24189.217 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01863*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-PNE / PARA-NITROPHENYL PHOSPHONOBUTANOYL L-ALANINE


Mass: 360.256 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H17N2O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.91 Å3/Da / Density % sol: 57 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: PEG600, ZnSO4, cacodylate, pH 7.00, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.5 / Details: Gigant, B., (1998) J. Mol. Biol., 284, 741.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
230 %(v/v)PEG6001reservoir
340 mMzinc acetate1reservoir
4100 mMcacodylate1reservoir

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: LURE / Beamline: DW32 / Wavelength: 0.963
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 8, 1998 / Details: BENT MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.963 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 43212 / Num. obs: 43212 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 26.3 Å2 / Rsym value: 0.07 / Net I/σ(I): 12
Reflection shellResolution: 1.9→1.93 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.0439 / % possible all: 97.6
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / Num. measured all: 111500 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 97.6 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.85refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YEC

1yec


Resolution: 1.9→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1900097.96 / Data cutoff high rms absF: 1900097.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.238 2198 5.1 %RANDOM
Rwork0.213 ---
obs-43201 95.4 %-
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.64 Å21.35 Å20 Å2
2--0.64 Å20 Å2
3----1.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3389 0 31 150 3570
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.01
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.7
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d28.6
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d1.58
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it1.791.5
X-RAY DIFFRACTIONo_mcangle_it2.942
X-RAY DIFFRACTIONo_scbond_it2.862
X-RAY DIFFRACTIONo_scangle_it4.162.5
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.293 314 5.8 %
Rwork0.293 5111 -
obs--97.6 %
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.213
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 33.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_angle_deg1.72
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_deg28.6
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_deg1.58
X-RAY DIFFRACTIONo_mcbond_it1.791.5
X-RAY DIFFRACTIONo_scbond_it2.862
X-RAY DIFFRACTIONo_mcangle_it2.942
X-RAY DIFFRACTIONo_scangle_it4.162.5
LS refinement shell
*PLUS
% reflection Rfree: 5.8 % / Rfactor Rwork: 0.293 / Rfactor obs: 0.293

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