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- PDB-2zck: Crystal structure of a ternary complex between PSA, a substrat-ac... -

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Basic information

Entry
Database: PDB / ID: 2zck
TitleCrystal structure of a ternary complex between PSA, a substrat-acyl intermediate and an activating antibody
Components
  • (monoclonal antibody 8G8F5 ...) x 2
  • KGISSQY
  • Prostate-specific antigen
KeywordsIMMUNE SYSTEM / human PSA / antibodies / kallikrein related peptidases / prostate cancer / Glycoprotein / Hydrolase / Protease / Secreted / Serine protease / Zymogen
Function / homology
Function and homology information


semenogelase / positive regulation of antibacterial peptide production / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / regulation of systemic arterial blood pressure / protein metabolic process / zymogen activation / serine-type peptidase activity / negative regulation of angiogenesis / secretory granule / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 ...semenogelase / positive regulation of antibacterial peptide production / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / regulation of systemic arterial blood pressure / protein metabolic process / zymogen activation / serine-type peptidase activity / negative regulation of angiogenesis / secretory granule / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / endopeptidase activity / serine-type endopeptidase activity / protein-containing complex / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Immunoglobulins / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Prostate-specific antigen
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMenez, R. / Stura, E. / Jolivet-Reynaud, C.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of a ternary complex between human prostate-specific antigen, its substrate acyl intermediate and an activating antibody
Authors: Michel, S. / Muller, B.H. / Bossus, M. / Ducancel, F. / Jolivet-Reynaud, C. / Stura, E.A.
History
DepositionNov 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_chiral / struct_asym / struct_conn / struct_ref_seq / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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.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_comp_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Prostate-specific antigen
S: KGISSQY
L: monoclonal antibody 8G8F5 Fab
H: monoclonal antibody 8G8F5 Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5595
Polymers75,1754
Non-polymers3831
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-18.7 kcal/mol
Surface area31090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.765, 86.765, 238.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Antibody , 2 types, 2 molecules LH

#3: Antibody monoclonal antibody 8G8F5 Fab


Mass: 23791.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascitic fluids / Source: (natural) Mus musculus (house mouse) / Strain: BALB/cjYco
#4: Antibody monoclonal antibody 8G8F5 Fab


Mass: 24479.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: ascitic fluids / Source: (natural) Mus musculus (house mouse) / Strain: BALB/cjYco

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Protein / Protein/peptide / Sugars / Non-polymers , 4 types, 34 molecules PS

#1: Protein Prostate-specific antigen / PSA / Kallikrein- 3 / Semenogelase / Gamma-seminoprotein / Seminin / P-30 antigen


Mass: 26122.025 Da / Num. of mol.: 1 / Fragment: UNP residues 25-261 / Source method: isolated from a natural source / Details: seminal fluids / Source: (natural) Homo sapiens (human) / References: UniProt: P07288, semenogelase
#2: Protein/peptide KGISSQY


Mass: 782.863 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsA SEQUENCE DATABASE REFERENCE FOR CHAIN L AND H DOES NOT CURRENTLY EXIST.

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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: 2.98 Å3/Da / Density % sol: 58.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: crystal grown in 14% MPEG550, 100mM HEPES (pH7.2), then soaked in PEG400, 100mM Tris-HCl (pH7.3), 10mM ZnCl2, 0.28 mg/ml Mu-KGISSQY-AFC, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.1→70.19 Å / Num. obs: 17100 / % possible obs: 99.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.115 / Rsym value: 0.127 / Net I/σ(I): 12.8
Reflection shellResolution: 3.1→3.27 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.3 / Num. unique all: 2397 / Rsym value: 0.583 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
MOSFLMdata reduction
PROCESSdata scaling
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2ZCH

2zch


Resolution: 3.1→70.19 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.862 / SU B: 22.086 / SU ML: 0.377 / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27522 870 5.1 %RANDOM
Rwork0.22064 ---
obs0.2234 16217 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 62.772 Å2
Baniso -1Baniso -2Baniso -3
1-1.11 Å20 Å20 Å2
2--1.11 Å20 Å2
3----2.22 Å2
Refinement stepCycle: LAST / Resolution: 3.1→70.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5273 0 25 31 5329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225437
X-RAY DIFFRACTIONr_bond_other_d0.0070.024732
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9587414
X-RAY DIFFRACTIONr_angle_other_deg0.974311094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3355688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73324.533214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.84915863
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0091521
X-RAY DIFFRACTIONr_chiral_restr0.2410.2835
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026031
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021035
X-RAY DIFFRACTIONr_nbd_refined0.2110.21199
X-RAY DIFFRACTIONr_nbd_other0.2010.25134
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22578
X-RAY DIFFRACTIONr_nbtor_other0.0910.23066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2130
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1610.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1730.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1361.54338
X-RAY DIFFRACTIONr_mcbond_other0.0641.51403
X-RAY DIFFRACTIONr_mcangle_it1.14925586
X-RAY DIFFRACTIONr_scbond_it1.57832318
X-RAY DIFFRACTIONr_scangle_it2.3424.51828
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 61 -
Rwork0.306 1143 -
obs-1143 98.37 %

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