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

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Basic information

Entry
Database: PDB / ID: 4uee
TitleCrystal structure of the human CARBOXYPEPTIDASE A1 in complex with the PHOSPHINIC INHIBITOR Acetyl-Leu-Ala-Y(PO2CH2)-homoPhe-OH
ComponentsCARBOXYPEPTIDASE A1
KeywordsHYDROLASE / 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-LA9 / Carboxypeptidase A1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 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 17, 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 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)70,4216
Polymers69,4102
Non-polymers1,0124
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-87.4 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.298, 83.983, 157.096
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 CARBOXYPEPTIDASE A1


Mass: 34704.840 Da / Num. of mol.: 2 / Fragment: CARBOXYPEPTIDASE DOMAIN, RESIDUES 111-4189
Source method: isolated from a genetically manipulated source
Details: IN COMPLEX WITH THE PHOSPHINIC INHIBITOR ACETYL-LEU-ALA-Y(PO2CH2)-HOMOPHE-OH.
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: PANCREAS / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): KM71H / References: UniProt: P15085, carboxypeptidase A
#2: Chemical ChemComp-LA9 / (2S)-2-{[(R)-{(1R)-1-[(N-acetyl-L-leucyl)amino]ethyl}(hydroxy)phosphoryl]methyl}-4-phenylbutanoic acid / Acetyl-Leu-Ala-y(PO2CH2)-homoPhe-OH


Mass: 440.470 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H33N2O6P
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.11 % / Description: NONE
Crystal growDetails: 0.2 M CALCIUM CHLORIDE, 0.1 M HEPES PH 7.0 AND 20% W/V PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979471
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979471 Å / Relative weight: 1
ReflectionResolution: 2.27→46.3 Å / Num. obs: 25246 / % possible obs: 86.6 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.2
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 5.3 / % possible all: 58.4

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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: 2.27→78.55 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.9 / SU B: 13.63 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22542 1279 5.1 %RANDOM
Rwork0.15371 ---
obs0.15743 23935 86.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.26 Å20 Å20 Å2
2---2.15 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.27→78.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4865 0 62 259 5186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225065
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.9446896
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5295611
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81923.921227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4715789
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4241519
X-RAY DIFFRACTIONr_chiral_restr0.1050.2755
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213865
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_it1.1481.53043
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.00924922
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.34932022
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0934.51974
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.74735065
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.27→2.329 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 54 -
Rwork0.179 861 -
obs--44.77 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0152-0.00150.0005-0.00010.00120.0345-0.00040.0001-0.0008-0.00150.00030.00130.0008-0.0010.00010.0583-0.0001-0.00020.0286-0.00020.0006-4.48091.9113-16.2291
20.0198-0.0102-0.00880.05860.00970.03140.00530.0023-0.0003-0.011-0.0043-0.0025-0.0024-0.0024-0.00110.05950.00010.0040.02730.0017-0.0002-11.928438.974-22.9249
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 308
2X-RAY DIFFRACTION2B3 - 308

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