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- PDB-3wab: Carboxypeptidase B in complex with DD2 -

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Basic information

Entry
Database: PDB / ID: 3wab
TitleCarboxypeptidase B in complex with DD2
ComponentsCarboxypeptidase B
KeywordsHYDROLASE/HYDROLASE INHIBITOR / CPB inhibitor / second zinc / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


carboxypeptidase B / metallocarboxypeptidase activity / cytoplasmic vesicle / proteolysis / extracellular space / zinc ion binding
Similarity search - Function
Carboxypeptidase B, 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 B, 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
CACODYLATE ION / (2R)-7-amino-2-(sulfanylmethyl)heptanoic acid / Carboxypeptidase B
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.154 Å
AuthorsYoshimoto, N. / Itoh, T. / Inaba, Y. / Yamamoto, K.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Structural basis for inhibition of carboxypeptidase B by selenium-containing inhibitor: selenium coordinates to zinc in enzyme.
Authors: Yoshimoto, N. / Itoh, T. / Inaba, Y. / Ishii, H. / Yamamoto, K.
History
DepositionMay 1, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,2646
Polymers34,7401
Non-polymers5255
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.314, 79.314, 100.342
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Carboxypeptidase B


Mass: 34739.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P09955, carboxypeptidase B
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DDW / (2R)-7-amino-2-(sulfanylmethyl)heptanoic acid


Mass: 191.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO2S
#4: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM sodium cacodylate (pH 5.3-6.8), 100mM zinc acetate, 5-15% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 86 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.541865 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 29, 2009
RadiationMonochromator: Varimax-HF, confocal multilayer mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541865 Å / Relative weight: 1
ReflectionResolution: 2.15→15 Å / Num. obs: 17871 / % possible obs: 99.5 %
Reflection shellResolution: 2.15→2.23 Å / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
d*TREKdata reduction
CNS1.3refinement
PDB_EXTRACT3.11data extraction
RAPID-AUTOdata collection
RAPID-AUTOdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZG7

1zg7


Resolution: 2.154→15 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2777 1786 10 %RANDOM
Rwork0.2067 16082 --
obs-17868 100 %-
Solvent computationBsol: 59.6371 Å2
Displacement parametersBiso max: 103.05 Å2 / Biso mean: 18.2892 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1-2.319 Å20 Å20 Å2
2--2.319 Å20 Å2
3----4.638 Å2
Refinement stepCycle: LAST / Resolution: 2.154→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 20 223 2679
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.0761.5
X-RAY DIFFRACTIONc_scbond_it1.7282
X-RAY DIFFRACTIONc_mcangle_it1.5452
X-RAY DIFFRACTIONc_scangle_it2.2892.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5carbohydrate.param
X-RAY DIFFRACTION6DD2.param
X-RAY DIFFRACTION7CAC.par

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