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- PDB-6i6z: Crystal structure of the human CARBOXYPEPTIDASE A1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6i6z
TitleCrystal structure of the human CARBOXYPEPTIDASE A1 in complex with the PHOSPHINIC INHIBITOR Acetyl-Tyr-Ala-Y(PO2CH2)-homoPhe-OH
ComponentsCarboxypeptidase A1
KeywordsHYDROLASE / Protease
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
Chem-TJE / Carboxypeptidase A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsGallego, P. / Reverter, D.
CitationJournal: J. Med. Chem. / Year: 2019
Title: Synthesis and Structural/Functional Characterization of Selective M14 Metallocarboxypeptidase Inhibitors Based on Phosphinic Pseudopeptide Scaffold: Implications on the Design of Specific Optical Probes.
Authors: Covaleda, G. / Gallego, P. / Vendrell, J. / Georgiadis, D. / Lorenzo, J. / Dive, V. / Aviles, F.X. / Reverter, D. / Devel, L.
History
DepositionNov 15, 2018Deposition site: PDBE / Processing site: PDBE
SupersessionDec 12, 2018ID: 4UEF
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 2.0Jan 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
Revision 2.1Feb 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.2Mar 13, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 2.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_label_asym_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)70,1956
Polymers69,0832
Non-polymers1,1124
Water6,467359
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-8 kcal/mol
Surface area22080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.121, 84.109, 158.195
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: 34541.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CPA1, CPA / Production host: Komagataella pastoris (fungus) / References: UniProt: P15085, carboxypeptidase A
#2: Chemical ChemComp-TJE / (2S)-2-{[(S)-{(1R)-1-[(N-acetyl-L-tyrosyl)amino]ethyl}(hydroxy)phosphoryl]methyl}-4-phenylbutanoic acid / Acetyl-Tyr-Ala-Y(PO2CH2)-homoPhe-OH


Mass: 490.486 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H31N2O7P / Feature type: SUBJECT OF INVESTIGATION
#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.: 359 / 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: 2.19 Å3/Da / Density % sol: 43.78 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1:1 (v:v) of hCPA1/8 complex at 16.1 mg/mL and a reservoir solution of 20% w/v PEG3350, 0.2 M MgCl 2 , 0.1 M HEPES, pH 6.0.

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.72→40.451 Å / Num. obs: 66309 / % possible obs: 99.94 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 1.33
Reflection shellResolution: 1.72→1.7446 Å / Rmerge(I) obs: 0.429

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOLREPphasing
SCALAdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KGQ

3kgq


Resolution: 1.72→40.44 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.15
RfactorNum. reflection% reflection
Rfree0.1833 3363 5.07 %
Rwork0.1582 --
obs0.1595 66309 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.72→40.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4935 0 0 359 5294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075136
X-RAY DIFFRACTIONf_angle_d1.1457001
X-RAY DIFFRACTIONf_dihedral_angle_d15.3951825
X-RAY DIFFRACTIONf_chiral_restr0.051764
X-RAY DIFFRACTIONf_plane_restr0.006888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.74460.20621380.16732571X-RAY DIFFRACTION100
1.7446-1.77060.20551420.15582597X-RAY DIFFRACTION100
1.7706-1.79830.21171120.15222601X-RAY DIFFRACTION100
1.7983-1.82780.19191410.14782587X-RAY DIFFRACTION100
1.8278-1.85930.20081380.14792573X-RAY DIFFRACTION100
1.8593-1.89310.20371560.15242561X-RAY DIFFRACTION100
1.8931-1.92950.18521380.14942630X-RAY DIFFRACTION100
1.9295-1.96890.18841440.15562551X-RAY DIFFRACTION100
1.9689-2.01170.20891490.15982619X-RAY DIFFRACTION100
2.0117-2.05850.16131490.15232551X-RAY DIFFRACTION100
2.0585-2.110.19621450.15472607X-RAY DIFFRACTION100
2.11-2.1670.20221410.15692590X-RAY DIFFRACTION100
2.167-2.23080.18421380.16122623X-RAY DIFFRACTION100
2.2308-2.30280.1831620.16412581X-RAY DIFFRACTION100
2.3028-2.38510.18491180.16452621X-RAY DIFFRACTION100
2.3851-2.48050.19091180.16852642X-RAY DIFFRACTION100
2.4805-2.59340.21430.17352639X-RAY DIFFRACTION100
2.5934-2.73010.18691440.17682626X-RAY DIFFRACTION100
2.7301-2.90110.19491360.17952652X-RAY DIFFRACTION100
2.9011-3.12510.2141340.17462625X-RAY DIFFRACTION100
3.1251-3.43940.19971280.17172673X-RAY DIFFRACTION100
3.4394-3.93670.17321500.15182664X-RAY DIFFRACTION100
3.9367-4.95840.11731480.12672711X-RAY DIFFRACTION100
4.9584-40.45130.1771510.14982851X-RAY DIFFRACTION100
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)
10.5253-0.0056-0.02120.60920.11640.7877-0.00850.0286-0.0455-0.0193-0.00280.00510.0279-0.04080.0120.05190.00320.00310.0565-0.00310.0598-4.65271.7381-16.512
20.51540.0387-0.13961.0447-0.11240.76730.00290.0410.0414-0.02430.03010.0729-0.0506-0.0572-0.02630.05520.00940.00690.06390.01260.0682-12.27638.7054-23.0598
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq -10:9999)
2X-RAY DIFFRACTION2(chain B and resseq -10:9999)

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