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- PDB-1eap: CRYSTAL STRUCTURE OF A CATALYTIC ANTIBODY WITH A SERINE PROTEASE ... -

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Basic information

Entry
Database: PDB / ID: 1eap
TitleCRYSTAL STRUCTURE OF A CATALYTIC ANTIBODY WITH A SERINE PROTEASE ACTIVE SITE
Components
  • IGG2B-KAPPA 17E8 FAB (HEAVY CHAIN)
  • IGG2B-KAPPA 17E8 FAB (LIGHT CHAIN)
KeywordsCATALYTIC ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHENYL[1-(N-SUCCINYLAMINO)PENTYL]PHOSPHONATE / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsZhou, G.W. / Guo, J. / Huang, W. / Scanlan, T.S. / Fletterick, R.J.
Citation
Journal: Science / Year: 1994
Title: Crystal structure of a catalytic antibody with a serine protease active site.
Authors: Zhou, G.W. / Guo, J. / Huang, W. / Scanlan, T.S. / Fletterick, R.J.
#1: Journal: J.Am.Chem.Soc. / Year: 1994
Title: Kinetic and Mechanistic Characterization of an Efficient Hydrolytic Antibody: Evidence for the Formation of an Acyl Intermediate
Authors: Guo, J. / Huang, W. / Scanlan, T.S.
History
DepositionAug 10, 1994Processing site: BNL
Revision 1.0Dec 20, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _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 / 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: IGG2B-KAPPA 17E8 FAB (LIGHT CHAIN)
B: IGG2B-KAPPA 17E8 FAB (HEAVY CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7583
Polymers46,4152
Non-polymers3431
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-22 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.410, 78.060, 81.940
Angle α, β, γ (deg.)90.00, 94.94, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO A 8 / 2: CIS PROLINE - PRO A 141 / 3: CIS PROLINE - PRO B 158
4: VAL B 194 - PRO B 195 OMEGA = 230.46 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Antibody IGG2B-KAPPA 17E8 FAB (LIGHT CHAIN)


Mass: 23528.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: GenBank: 12002896
#2: Antibody IGG2B-KAPPA 17E8 FAB (HEAVY CHAIN)


Mass: 22886.492 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-HEP / PHENYL[1-(N-SUCCINYLAMINO)PENTYL]PHOSPHONATE


Mass: 343.312 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22NO6P
Has protein modificationY
Sequence detailsTHE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM THE DNA SEQUENCE OF GUO ET AL., 1994, ...THE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DERIVED FROM THE DNA SEQUENCE OF GUO ET AL., 1994, LISTED IN REFERENCE 1 ABOVE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
24.5 mMhapten 41drop
30.1 MHEPES1reservoir
415 %PEG40001reservoir
55 %isopropanol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. obs: 13531 / Num. measured all: 34177 / Rmerge(I) obs: 0.076

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.4→6 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.186 -
obs0.186 13531
Refinement stepCycle: LAST / Resolution: 2.4→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3264 0 23 0 3287
Refine LS restraints
Refine-IDTypeDev ideal
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_deg3.078
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.186 / Highest resolution: 2.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.078

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