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- PDB-2v77: Crystal Structure of Human Carboxypeptidase A1 -

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Basic information

Entry
Database: PDB / ID: 2v77
TitleCrystal Structure of Human Carboxypeptidase A1
ComponentsCARBOXYPEPTIDASE A1
KeywordsHYDROLASE / METAL-BINDING / METALLOPROTEASE / CARBOXYPEPTIDASE / PROTEIN DEGRADATION / ZINC / ZYMOGEN / PROTEASE / SECRETED
Function / homology
Function and homology information


carboxypeptidase A / leukotriene metabolic process / metallocarboxypeptidase activity / response to cadmium ion / proteolysis involved in protein catabolic process / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase ...Carboxypeptidase A, carboxypeptidase domain / Carboxypeptidase, activation peptide / Metallocarboxypeptidase-like, propeptide / Carboxypeptidase activation peptide / Zinc carboxypeptidases, zinc-binding region 2 signature. / Zinc carboxypeptidases, zinc-binding region 1 signature. / Peptidase family M14 domain profile. / Zn_pept / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
OCTANE-1,3,5,7-TETRACARBOXYLIC ACID / Carboxypeptidase A1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.603 Å
AuthorsPallares, I. / Fernandez, D. / Comellas-Bigler, M. / Fernandez-Recio, J. / Ventura, S. / Aviles, F.X. / Vendrell, J.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2008
Title: Direct interaction between a human digestive protease and the mucoadhesive poly(acrylic acid).
Authors: Pallares, I. / Fernandez, D. / Comellas-Bigler, M. / Fernandez-Recio, J. / Ventura, S. / Aviles, F.X. / Bode, W. / Vendrell, J.
History
DepositionJul 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 19, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBOXYPEPTIDASE A1
B: CARBOXYPEPTIDASE A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,8369
Polymers69,4102
Non-polymers1,4267
Water13,998777
1
A: CARBOXYPEPTIDASE A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5375
Polymers34,7051
Non-polymers8324
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: CARBOXYPEPTIDASE A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2994
Polymers34,7051
Non-polymers5943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)129.565, 129.565, 90.856
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein CARBOXYPEPTIDASE A1


Mass: 34704.840 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: PANCREAS / Plasmid: PPIC9 / Production host: PICHIA PASTORIS (fungus) / Strain (production host): KM 71 / References: UniProt: P15085, EC: 3.14.17.1
#2: Chemical ChemComp-PAY / OCTANE-1,3,5,7-TETRACARBOXYLIC ACID / (3R,5R,7S)-OCTANE-1,3,5,7-TETRACARBOXYLIC ACID


Mass: 290.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H18O8
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 777 / Source method: isolated from a natural source / Formula: H2O

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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: 2.75 Å3/Da / Density % sol: 55.22 % / Description: NONE
Crystal growpH: 7.5
Details: 22% (W/V) PAY 5100, HEPES 0.1 M, MAGNESIUM CHLORIDE 0.02 M (PH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 101271 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.5
Reflection shellResolution: 1.6→1.68 Å / % possible all: 83.1

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Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5CPA

5cpa


Resolution: 1.603→20 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 2012 2 %RANDOM
Rwork0.1782 ---
obs0.1782 100653 99.4 %-
Solvent computationBsol: 56.6892 Å2 / ksol: 0.343549 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.888 Å2--
2---1.888 Å2-
3---3.777 Å2
Refinement stepCycle: LAST / Resolution: 1.603→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4886 0 87 777 5750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3832
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1HEPES.PARHEPES.TOP
X-RAY DIFFRACTION2CNS_TOPPAR.WATER_REP.PARAMCNS_TOPPAR.WATER.TOP
X-RAY DIFFRACTION3CNS_TOPPAR.ION.PARAM
X-RAY DIFFRACTION5PAA.PAR
X-RAY DIFFRACTION4CNS_TOPPAR.ION.TOP
X-RAY DIFFRACTION6PAA.TOP

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