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

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Basic information

Entry
Database: PDB / ID: 2pja
TitleCRYSTAL STRUCTURE OF ACTIVATED PORCINE PANCREATIC CARBOXYPEPTIDASE B 3-{[(R)-1-((S)-2-Benzyloxycarbonylamino-3-phenyl-propionylamino)-2-methyl-propyl]-hydroxy-phosphinoyl}-2-(3-guanidino-phenyl)-propionic 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. / 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-33Z / Carboxypeptidase B
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxypeptidase B
B: Carboxypeptidase B
C: Carboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2879
Polymers104,2203
Non-polymers2,0676
Water11,241624
1
A: Carboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4293
Polymers34,7401
Non-polymers6892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4293
Polymers34,7401
Non-polymers6892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4293
Polymers34,7401
Non-polymers6892
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.964, 96.379, 135.641
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 B /


Mass: 34739.859 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-33Z / (2S)-2-(3-{[AMINO(IMINO)METHYL]AMINO}PHENYL)-3-[(R)-[(1R)-1-({N-[(BENZYLOXY)CARBONYL]-L-PHENYLALANYL}AMINO)-2-METHYLPROPYL](HYDROXY)PHOSPHORYL]PROPANOIC ACID


Mass: 623.636 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C31H38N5O7P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 2.1 Å3/Da / Density % sol: 41.41 %
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: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 24, 2001 / Details: SI(111)
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.7→21.4 Å / Num. obs: 93217 / % possible obs: 96.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 17.6 Å2 / Rsym value: 0.087 / Net I/σ(I): 7.2
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.353 / % possible all: 89.1

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Processing

Software
NameVersionClassification
X-PLORmodel building
CNX2005refinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1Z5R

1z5r


Resolution: 1.7→21.4 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2421454.56 / 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
Rfree0.219 3653 4 %RANDOM
Rwork0.189 ---
obs0.19 92221 94.8 %-
all-93160 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.4 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 21.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20 Å20 Å2
2--6.78 Å20 Å2
3----7.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→21.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7308 0 135 624 8067
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
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_deg0.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.1
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_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.522
X-RAY DIFFRACTIONc_scbond_it1.862
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 1.7→1.76 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.273 316 3.8 %
Rwork0.249 8040 -
obs--87.3 %
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 DIFFRACTION4333.PAR333.TOP

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