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- PDB-4uez: Crystal structure of the human CARBOXYPEPTIDASE A1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4uez
TitleCrystal structure of the human CARBOXYPEPTIDASE A1 in complex with the PHOSPHINIC INHIBITOR Acetyl-Leu-Phe-Y(PO2CH2)-Phe-OH
ComponentsHUMAN CARBOXYPEPTIDASE A1
KeywordsHYDROLASE / CARBOXYPEPTIDASE / CPA1 / PHOSPHINIC INHIBITOR
Function / homology
Function and homology information


carboxypeptidase A / leukotriene metabolic process / Developmental Lineage of Pancreatic Acinar Cells / response to cadmium ion / metallocarboxypeptidase activity / 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. / Zn_pept / Peptidase family M14 domain profile. / 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. / Zn_pept / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zinc carboxypeptidase / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-LFF / Carboxypeptidase A1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsGallego, P. / Covaleda, G. / Costenaro, L. / Devel, L. / Dive, V. / Aviles, F.X. / Reverter, D.
CitationJournal: To be Published
Title: Crystal Structure of the Human Carboxypeptidase A1 in Complex with Phosphinic Inhibitors
Authors: Gallego, P. / Covaleda, G. / Devel, L. / Dive, V. / Aviles, F.X. / Reverter, D.
History
DepositionDec 22, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...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 / 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,5466
Polymers69,4102
Non-polymers1,1364
Water4,990277
1
A: HUMAN CARBOXYPEPTIDASE A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2733
Polymers34,7051
Non-polymers5682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HUMAN CARBOXYPEPTIDASE A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2733
Polymers34,7051
Non-polymers5682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.989, 84.143, 158.005
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein HUMAN CARBOXYPEPTIDASE A1


Mass: 34704.840 Da / Num. of mol.: 2 / Fragment: CARBOXYPEPTIDASE DOMAIN, UNP RESIDUES 111-419
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: PANCREATIC / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): KM71H / References: UniProt: P15085, carboxypeptidase A
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-LFF / (2S)-3-[(R)-{(1R)-1-[(N-acetyl-L-leucyl)amino]-2-phenylethyl}(hydroxy)phosphoryl]-2-benzylpropanoic acid / ACETYL-LEU-PHE-Y(PO2CH2)-PHE-OH


Mass: 502.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H35N2O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.2 Å3/Da / Density % sol: 44.19 % / Description: NONE
Crystal growDetails: 0.2 M CALCIUM CHLORIDE, 0.1 M HEPES PH 7.0 AND 17% W/V PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979493
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979493 Å / Relative weight: 1
ReflectionResolution: 2.29→45.99 Å / Num. obs: 28256 / % possible obs: 98.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.3
Reflection shellResolution: 2.29→2.41 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 8.1 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XPSdata reduction
CCP4Idata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V77

2v77


Resolution: 2.29→79 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.232 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20519 1408 5 %RANDOM
Rwork0.15036 ---
obs0.15317 26789 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.005 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2---0.33 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.29→79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4865 0 72 277 5214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225112
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9396966
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4345619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.30824230
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90415795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9251519
X-RAY DIFFRACTIONr_chiral_restr0.1210.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213923
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9291.53067
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70224966
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.82832045
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4274.52000
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.288→2.347 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.206 72 -
Rwork0.153 1657 -
obs--93.81 %

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