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- PDB-2jew: Crystal structure of ((2S)-5-amino-2-((1-n-propyl-1H-imidazol-4-y... -

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Basic information

Entry
Database: PDB / ID: 2jew
TitleCrystal structure of ((2S)-5-amino-2-((1-n-propyl-1H-imidazol-4-yl) methyl)pentanoic acid) UK396,082 a TAFIa inhibitor, Bound to Activated Porcine Pancreatic carboxypeptidaseB
ComponentsCARBOXYPEPTIDASE BCarboxypeptidase
KeywordsHYDROLASE / CARBOXYPEPTIDASE / CARBOXYPEPTIDASE B / DIRECT METAL-BINDING / METALLOPROTEASE / PROTEASE / ZINC / ZYMOGEN / EXOPEPTIDASE
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
Chem-720 / Carboxypeptidase B
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBrown, D.G. / Moore, R.S.
CitationJournal: J. Med. Chem. / Year: 2007
Title: Discovery of potent & selective inhibitors of activated thrombin-activatable fibrinolysis inhibitor for the treatment of thrombosis.
Authors: Bunnage, M.E. / Blagg, J. / Steele, J. / Owen, D.R. / Allerton, C. / McElroy, A.B. / Miller, D. / Ringer, T. / Butcher, K. / Beaumont, K. / Evans, K. / Gray, A.J. / Holland, S.J. / Feeder, N. ...Authors: Bunnage, M.E. / Blagg, J. / Steele, J. / Owen, D.R. / Allerton, C. / McElroy, A.B. / Miller, D. / Ringer, T. / Butcher, K. / Beaumont, K. / Evans, K. / Gray, A.J. / Holland, S.J. / Feeder, N. / Moore, R.S. / Brown, D.G.
History
DepositionJan 24, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_detector
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_detector.type
Revision 1.4Dec 13, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn
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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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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)35,1104
Polymers34,7401
Non-polymers3703
Water5,477304
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)84.090, 84.090, 92.820
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 / Carboxypeptidase / ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B


Mass: 34739.859 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 111-416 / Source method: isolated from a natural source / Details: PURCHASED / Source: (natural) SUS SCROFA (pig) / Tissue: PANCREATICPancreas / References: UniProt: P09955, carboxypeptidase B
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-720 / (2S)-5-AMINO-2-[(1-PROPYL-1H-IMIDAZOL-4-YL)METHYL]PENTANOIC ACID


Mass: 239.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21N3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFROM PATENT PUBLICATION US 5672496-A

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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: 2.36 Å3/Da / Density % sol: 47.85 % / Description: 1NSA HAS WRONG PORCINE CPB SEQUENCE
Crystal growpH: 7.4
Details: 100 MM NAKPO4 PH6.8 AND 200 MM ZINC ACETATE, 10% PEG 8000, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 28, 2000 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.4→29 Å / Num. obs: 66699 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 5.6 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC4.0.2refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NSA

1nsa


Resolution: 1.4→29 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 3100 5 %RANDOM
Rwork0.19 ---
obs0.19 58036 99.8 %-
Refinement stepCycle: LAST / Resolution: 1.4→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2436 0 19 304 2759

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