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- PDB-1iy7: Crystal Structure of CPA and sulfamide-based inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 1iy7
TitleCrystal Structure of CPA and sulfamide-based inhibitor complex
ComponentsCarboxypeptidase A
KeywordsHYDROLASE / Protein-Inhibitor complex
Function / homology
Function and homology information


carboxypeptidase A / leukotriene metabolic process / metallocarboxypeptidase activity / 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
PHENYLALANINE-N-SULFONAMIDE / Carboxypeptidase A1
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsKim, S.J. / Woo, J.R. / Park, J.D. / Kim, D.H. / Ryu, S.E.
CitationJournal: J.Med.Chem. / Year: 2002
Title: Sulfamide-Based Inhibitors for Carboxypeptidase A. Novel Type Transition State Analogue Inhibitors for Zinc Proteases
Authors: Park, J.D. / Kim, D.H. / Kim, S.J. / Woo, J.R. / Ryu, S.E.
History
DepositionJul 24, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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 1.4Oct 23, 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: Carboxypeptidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7523
Polymers34,4421
Non-polymers3102
Water2,666148
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.688, 60.467, 47.256
Angle α, β, γ (deg.)90.00, 82.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carboxypeptidase A


Mass: 34442.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00730, carboxypeptidase A
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CXA / PHENYLALANINE-N-SULFONAMIDE


Mass: 244.268 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12N2O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.13 Å3/Da / Density % sol: 42.13 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
11.2 M11LiCl
220 mMTris-HCl11pH7.5
30.2 M12LiCl
420 mMTris-HCl12pH7.5

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Details: confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→26.04 Å / Num. all: 19491 / Num. obs: 19491 / Observed criterion σ(F): 0 / Biso Wilson estimate: 13.3 Å2 / Limit h max: 25 / Limit h min: -25 / Limit k max: 30 / Limit k min: -25 / Limit l max: 23 / Limit l min: 0 / Observed criterion F max: 1152831.55 / Observed criterion F min: 15.5
Reflection
*PLUS
Lowest resolution: 99 Å / % possible obs: 99.2 % / Rmerge(I) obs: 0.108

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
CNS0.9refinement
CCP4(SCALA)data scaling
RefinementResolution: 2→26.04 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.208 945 4.8 %random
Rwork0.175 ---
obs0.175 19491 99.3 %-
all-19633 --
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 44.7156 Å2 / ksol: 0.309186 e/Å3
Displacement parametersBiso max: 50.57 Å2 / Biso mean: 18.38 Å2 / Biso min: 8.23 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å2-0.86 Å2
2---1.2 Å20 Å2
3---1.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.15 Å
Luzzati d res high-2
Refinement stepCycle: LAST / Resolution: 2→26.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 17 148 2601
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle1.2
X-RAY DIFFRACTIONx_torsion23.2
X-RAY DIFFRACTIONx_torsion_impr0.71
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2-2.090.2131174.80.21722800.022431239798.6
2.09-2.20.1951154.70.19422860.0182434240198.6
2.2-2.340.1921255.10.18923190.0172469244498.9
2.34-2.520.1791235.10.17722790.0162417240299.4
2.52-2.770.2011174.80.223250.0192454244299.5
2.77-3.170.1941124.60.19123300.0182445244299.8
3.17-40.1621114.50.15723610.0152475247299.9
4-26.040.14512550.14823660.0132506249199.4
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 99 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.71

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