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

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Basic information

Entry
Database: PDB / ID: 6skh
TitleX-ray structure of human glutamate carboxypeptidase II (GCPII) - the E424M inactive mutant, in complex with a inhibitor sulfamide inhibitor GluAsp
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 / carboxypeptidase activity / metallocarboxypeptidase 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 / carboxypeptidase activity / metallocarboxypeptidase activity / peptidase activity / cell surface / proteolysis / extracellular exosome / metal ion binding / membrane / 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
beta-D-mannopyranose / Chem-LHK / DI(HYDROXYETHYL)ETHER / Glutamate carboxypeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.58 Å
AuthorsMotlova, L. / Novakova, Z. / Barinka, C.
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 15, 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)84,32920
Polymers79,6171
Non-polymers4,71319
Water10,647591
1
A: Glutamate carboxypeptidase 2
hetero molecules

A: Glutamate carboxypeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,65940
Polymers159,2342
Non-polymers9,42538
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area16470 Å2
ΔGint86 kcal/mol
Surface area51230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.629, 130.530, 159.192
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
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 , 6 types, 8 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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.: 2
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
#4: 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
#5: 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
#6: 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.: 2
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
#11: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 8 types, 602 molecules

#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#12: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#13: Chemical ChemComp-LHK / (2~{S})-2-[[(2~{S})-1,4-bis(oxidanyl)-1,4-bis(oxidanylidene)butan-2-yl]sulfamoylamino]pentanedioic acid


Mass: 342.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O10S
#14: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 3.36 Å3/Da / Density % sol: 63.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 33% (v/v) pentaerythritol propoxylate PO/OH 5/4, 2 % (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 PILATUS 6M / Detector: PIXEL / Date: Oct 31, 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: 143110 / % possible obs: 99.2 % / Redundancy: 4.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.033 / Rrim(I) all: 0.042 / Net I/σ(I): 19.5
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.528 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 29834 / CC1/2: 0.86 / Rrim(I) all: 0.678 / % possible all: 97.8

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Processing

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

3bi1


Resolution: 1.58→49.21 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.965 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.071
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1928 7026 4.9 %RANDOM
Rwork0.1712 ---
obs0.1722 136083 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 128.96 Å2 / Biso mean: 29.211 Å2 / Biso min: 14.54 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2---2.03 Å20 Å2
3---0.7 Å2
Refinement stepCycle: final / Resolution: 1.58→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5545 0 300 591 6436
Biso mean--52.88 39.37 -
Num. residues----696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0156664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175833
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.829092
X-RAY DIFFRACTIONr_angle_other_deg4.2111.77913821
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1885810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96320.915284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2315986
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.851538
X-RAY DIFFRACTIONr_chiral_restr0.0830.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217530
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021281
X-RAY DIFFRACTIONr_mcbond_it1.5152.7613105
X-RAY DIFFRACTIONr_mcbond_other1.5152.7613104
X-RAY DIFFRACTIONr_mcangle_it2.2674.1443958
LS refinement shellResolution: 1.58→1.62 Å
RfactorNum. reflection% reflection
Rfree0.298 513 -
Rwork0.278 9899 -
obs--98.27 %

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