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- PDB-6sgp: X-ray structure of human glutamate carboxypeptidase II (GCPII) - ... -

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Basic information

Entry
Database: PDB / ID: 6sgp
TitleX-ray structure of human glutamate carboxypeptidase II (GCPII) - the E424M inactive mutant, in complex with a sulfamide inhibitor GluGlu
ComponentsGlutamate carboxypeptidase 2
KeywordsHYDROLASE / glutamate carboxypeptidase II (GCPII) / NAALADase / prostate-specific membrane antigen / sulfamide
Function / homology
Function and homology information


Ac-Asp-Glu binding / tetrahydrofolyl-poly(glutamate) polymer binding / glutamate carboxypeptidase II / folic acid-containing compound metabolic process / C-terminal protein deglutamylation / Aspartate and asparagine metabolism / dipeptidase activity / metallocarboxypeptidase activity / carboxypeptidase activity / peptidase activity ...Ac-Asp-Glu binding / tetrahydrofolyl-poly(glutamate) polymer binding / glutamate carboxypeptidase II / folic acid-containing compound metabolic process / C-terminal protein deglutamylation / Aspartate and asparagine metabolism / dipeptidase activity / metallocarboxypeptidase activity / carboxypeptidase activity / peptidase activity / cell surface / proteolysis / extracellular exosome / membrane / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / PA domain superfamily / PA domain / PA domain / Peptidase M28 / Peptidase family M28
Similarity search - Domain/homology
Chem-LDK / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Glutamate carboxypeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.58 Å
AuthorsBarinka, C. / Shukla, S. / Motlova, L.
CitationJournal: J.Chem.Inf.Model. / Year: 2024
Title: Structural, Biochemical, and Computational Characterization of Sulfamides as Bimetallic Peptidase Inhibitors.
Authors: Novakova, Z. / Tehrani, Z.A. / Jurok, R. / Motlova, L. / Kutil, Z. / Pavlicek, J. / Shukla, S. / Choy, C.J. / Havlinova, B. / Baranova, P. / Berkman, C.E. / Kuchar, M. / Cerny, J. / Barinka, C.
History
DepositionAug 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutamate carboxypeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,14317
Polymers79,6171
Non-polymers4,52616
Water7,819434
1
A: Glutamate carboxypeptidase 2
hetero molecules

A: Glutamate carboxypeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,28634
Polymers159,2342
Non-polymers9,05332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area15040 Å2
ΔGint52 kcal/mol
Surface area51200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.349, 130.394, 158.538
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Glutamate carboxypeptidase 2 / Cell growth-inhibiting gene 27 protein / Folate hydrolase 1 / Folylpoly-gamma-glutamate ...Cell growth-inhibiting gene 27 protein / Folate hydrolase 1 / Folylpoly-gamma-glutamate carboxypeptidase / FGCP / Glutamate carboxypeptidase II / GCPII / Membrane glutamate carboxypeptidase / mGCP / N-acetylated-alpha-linked acidic dipeptidase I / NAALADase I / Prostate-specific membrane antigen / PSMA / Pteroylpoly-gamma-glutamate carboxypeptidase


Mass: 79616.828 Da / Num. of mol.: 1 / Mutation: E424M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOLH1, FOLH, NAALAD1, PSM, PSMA, GIG27 / Production host: Drosophila melanogaster (fruit fly) / Variant (production host): Schneiders S2 cells / References: UniProt: Q04609, glutamate carboxypeptidase II

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Sugars , 4 types, 7 molecules

#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 8 types, 443 molecules

#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#11: Chemical ChemComp-LDK / (2~{S})-2-[[(2~{S})-1,5-bis(oxidanyl)-1,5-bis(oxidanylidene)pentan-2-yl]sulfamoylamino]pentanedioic acid


Mass: 356.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O10S / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.36 Å3/Da / Density % sol: 63.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 33% (v/v) pentaerythritol propoxylate PO/OH 5/4 1 % (w/v) PEG 3350 100 mM Tris-HCl, pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 141047 / % possible obs: 97 % / Redundancy: 4.4 % / CC1/2: 1 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.045 / Net I/σ(I): 18.5
Reflection shellResolution: 1.58→1.67 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.689 / Num. unique obs: 22618 / CC1/2: 0.83 / Rrim(I) all: 0.789 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PDB_EXTRACT3.22data extraction
Aimlessdata scaling
REFMACphasing
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3BI1

3bi1


Resolution: 1.58→46.9 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.072
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2011 7094 5 %RANDOM
Rwork0.1803 ---
obs0.1813 134096 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 122.4 Å2 / Biso mean: 30.564 Å2 / Biso min: 16.38 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2---2.23 Å20 Å2
3---0.73 Å2
Refinement stepCycle: final / Resolution: 1.58→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5511 0 289 434 6234
Biso mean--54.15 37.9 -
Num. residues----692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0156330
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175532
X-RAY DIFFRACTIONr_angle_refined_deg1.3541.8228607
X-RAY DIFFRACTIONr_angle_other_deg4.2871.77913095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2255746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1621.222270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53515924
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9791533
X-RAY DIFFRACTIONr_chiral_restr0.0840.2823
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217022
X-RAY DIFFRACTIONr_gen_planes_other0.0140.021210
X-RAY DIFFRACTIONr_mcbond_it1.7162.9052927
X-RAY DIFFRACTIONr_mcbond_other1.7152.9062928
X-RAY DIFFRACTIONr_mcangle_it2.4794.353690
LS refinement shellResolution: 1.58→1.619 Å
RfactorNum. reflection% reflection
Rfree0.341 493 -
Rwork0.334 9735 -
obs--97.04 %

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