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- PDB-1zg7: Crystal Structure of 2-(5-{[amino(imino)methyl]amino}-2-chlorophe... -

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Basic information

Entry
Database: PDB / ID: 1zg7
TitleCrystal Structure of 2-(5-{[amino(imino)methyl]amino}-2-chlorophenyl)-3-sulfanylpropanoic acid Bound to Activated Porcine Pancreatic Carboxypeptidase B
Componentsprocarboxypeptidase B
KeywordsHYDROLASE / CARBOXYPEPTIDASE B / EXOPEPTIDASE / thiol 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-P20 / Carboxypeptidase B
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsAdler, M. / Bryant, J. / Buckman, B. / Islam, I. / Larsen, B. / Finster, S. / Kent, L. / May, K. / Mohan, R. / Yuan, S. / Whitlow, M.
CitationJournal: 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.
History
DepositionApr 20, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / 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
Remark 600HETEROGEN THE INHIBITION CONSTANT (KI APPARENT) OF 2-(5-{[AMINO (IMINO)METHYL] AMINO}-2- ...HETEROGEN THE INHIBITION CONSTANT (KI APPARENT) OF 2-(5-{[AMINO (IMINO)METHYL] AMINO}-2-CHLOROPHENYL)-3-SULFANYLPROPANOIC ACID WAS MEASURED AS 7 NM AGAINST PORCINE PANCREATIC CARBOXYPEPTIDASE B. THE ASSAY FOR INHIBITION OF PORCINE PANCREATIC CPB (SIGMA, ST. LOUIS, MO) WAS PERFORMED IN A 96 OR 384-WELL FORMAT ADAPTED FROM PUBLISHED PROTOCOLS. PURIFIED PP-CPB (2 NM) WAS INCUBATED WITH TEST COMPOUNDS IN 20 MM HEPES PH 7.4, 150 MM NACL, 5 MM CACL2 FOR 2 MINUTES PRIOR TO THE ADDITION OF THE 0.6 MM HIPPURYL-L -ARGININE SUBSTRATE. AFTER 30 MINUTES AT ROOM TEMPERATURE, THE AMOUNT OF SUBSTRATE HYDROLYZED WAS DETERMINED BY CONVERSION OF THE PRODUCT, HIPPURIC ACID, TO A CHROMOGEN WITH SODIUM PHOSPHATE BUFFER, PH 8.3 (F.C. 0.8 MM) AND CYANURIC CHLORIDE/DIOXANE (F.C. 0.9% W/V) UNDER CHEMICAL FUME HOOD. FOLLOWING CENTRIFUGATION OF THE MICROTITER PLATES AND TRANSFER OF THE SUPERNATANT TO A CLEAN PLATE, ABSORBANCE OF THE SUPERNATANT IS READ AT 382 NM. THE IC50 OF THE COMPOUND WAS DETERMINED USING THE 4-PARAMETER EQUATION FROM AN 8-POINT DOSE RESPONSE CURVE, EACH COMPOUND TESTED IN DUPLICATE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)105,2379
Polymers104,2203
Non-polymers1,0176
Water11,620645
1
A: procarboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0793
Polymers34,7401
Non-polymers3392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: procarboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0793
Polymers34,7401
Non-polymers3392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: procarboxypeptidase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0793
Polymers34,7401
Non-polymers3392
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.504, 100.369, 136.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer that can be generated from either chain A, chain B, or chain C.

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Components

#1: Protein procarboxypeptidase 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-P20 / 2-(5-{[AMINO(IMINO)METHYL]AMINO}-2-CHLOROPHENYL)-3-SULFANYLPROPANOIC ACID


Mass: 273.739 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12ClN3O2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 645 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
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 / Wavelength: 1.08 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 7, 2000
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.081
21.081
ReflectionResolution: 1.75→20 Å / Num. obs: 93605 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 24.9 Å2 / Rsym value: 0.068 / Net I/σ(I): 6.6
Reflection shellResolution: 1.75→1.83 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 11051 / Rsym value: 0.36 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
X-PLOR3.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NAS CATALYTIC DOMAIN

1nas


Resolution: 1.75→8 Å / Isotropic thermal model: OVERALL / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3473 -RANDOM
Rwork0.208 ---
all0.213 92660 --
obs0.211 90906 99.9 %-
Displacement parametersBiso mean: 29.25 Å2
Baniso -1Baniso -2Baniso -3
1--4.8686 Å20 Å20 Å2
2---4.6192 Å20 Å2
3---9.4878 Å2
Refinement stepCycle: LAST / Resolution: 1.75→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7320 0 54 645 8019
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.81
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.42
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.75-1.830.33773983.70.36551065311051100
1.83-1.920.3464130.323611107100
1.92-2.040.31164330.28711194100
2.04-2.20.29164210.257111276100
2.2-2.410.26784540.23711368100
2.41-2.750.24954490.215911440100
2.75-3.420.274540.191158699.9
3.42-80.23244510.15861188499.9

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