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- PDB-2pj4: CRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDAS... -

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Basic information

Entry
Database: PDB / ID: 2pj4
TitleCRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B [((R)-Benzyloxycarbonylamino-cyclohexyl-methyl)-hydroxy-phosphinoyloxy]-(3-guanidino-phenyl)-acetic acid COMPLEX
ComponentsCarboxypeptidase B
KeywordsHYDROLASE / CARBOXYPEPTIDASE B / EXOPEPTIDASE / Phosphinate BASED INHIBITOR
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. / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A ...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. / Zn_pept / Zinc carboxypeptidase / Peptidase family M14 domain profile. / Peptidase M14, carboxypeptidase A / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-414 / Carboxypeptidase B
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAdler, M. / Whitlow, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structures of potent selective peptide mimetics bound to carboxypeptidase B.
Authors: Adler, M. / Buckman, B. / Bryant, J. / Chang, Z. / Chu, K. / Emayan, K. / Hrvatin, P. / Islam, I. / Morser, J. / Sukovich, D. / West, C. / Yuan, S. / Whitlow, M.
#1: Journal: Biochemistry / Year: 2005
Title: Crystal Structures of Potent Thiol-Based Inhibitors Bound to Carboxypeptidase B.
Authors: Adler, M. / Bryant, J. / Buckman, B. / Islam, I. / Larsen, B. / Finster, S. / Kent, L. / May, K. / Mohan, R. / Yuan, S. / Whitlow, M.
#2: Journal: Bioorg.Med.Chem.Lett. / Year: 2007
Title: 3-Mercaptopropionic acids as efficacious inhibitors of activated thrombin activatable fibrinolysis inhibitor (TAFIa).
Authors: Islam, I. / Bryant, J. / May, K. / Mohan, R. / Yuan, S. / Kent, L. / Morser, J. / Zhao, L. / Vergona, R. / White, K. / Adler, M. / Whitlow, M. / Buckman, B.O.
History
DepositionApr 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 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 B
B: Carboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6486
Polymers69,4802
Non-polymers1,1684
Water5,242291
1
A: Carboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3243
Polymers34,7401
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3243
Polymers34,7401
Non-polymers5842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.069, 90.069, 173.666
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.: 2 / Fragment: CATALYTIC DOMAIN / 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.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-414 / (5R,6R,8S)-8-(3-{[AMINO(IMINO)METHYL]AMINO}PHENYL)-5-CYCLOHEXYL-6-HYDROXY-3-OXO-1-PHENYL-2,7-DIOXA-4-AZA-6-PHOSPHANONAN-9-OIC ACID 6-OXIDE


Mass: 518.499 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H31N4O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: SODIUM CHLORIDE, TRIS, SODIUM CACODYLATE, PEG 8000, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 49034 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.66 % / Biso Wilson estimate: 10.8 Å2 / Rsym value: 0.1428 / Net I/σ(I): 9.28
Reflection shellResolution: 2→2.12 Å / Redundancy: 6.83 % / Mean I/σ(I) obs: 2.18 / Rsym value: 0.3807 / % possible all: 100

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNX2005refinement
X-GENdata reduction
X-GENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Z5R

1z5r


Resolution: 2→23.92 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 132154.7 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 1744 3.9 %RANDOM
Rwork0.215 ---
obs0.217 45086 91.8 %-
all-46575 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.72 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1--2.64 Å20 Å20 Å2
2---2.64 Å20 Å2
3---5.27 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→23.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4872 0 74 291 5237
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.752
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.542.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 260 4 %
Rwork0.263 6295 -
obs--81.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARWATER.TOP
X-RAY DIFFRACTION3ZN.PARZN.TOP
X-RAY DIFFRACTION4414.PAR414.TOP

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