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- PDB-4jyw: X-ray structure of human glutamate carboxypeptidase II (GCPII) in... -

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Basic information

Entry
Database: PDB / ID: 4jyw
TitleX-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with CTT1057
ComponentsGlutamate carboxypeptidase 2
KeywordsHYDROLASE / metallopeptidase
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 / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Transcription Elongation Factor S-II; Chain A ...Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain / Transferrin receptor-like, dimerisation domain superfamily / Glutamate carboxypeptidase 2-like / Transferrin receptor-like dimerisation domain / Glucose Oxidase; domain 1 - #30 / PA domain superfamily / PA domain / PA domain / Transcription Elongation Factor S-II; Chain A / Glucose Oxidase; domain 1 / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(bba) Sandwich / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-T57 / Glutamate carboxypeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.73 Å
AuthorsBarinka, C.
CitationJournal: To be Published
Title: A high affinity 18F-labeled phosphoramidate peptidomimetic inhibitor as a PSMA-targeted PET imaging agent for prostate cancer
Authors: Ganguly, T. / Dannoon, S. / Geruntho, J.G. / Hopkins, M.R. / Murphy, S. / Cahaya, H. / Blecha, J.E. / Jivan, S. / Barinka, C. / Jones, E.F. / VanBrocklin, H.F. / Berkman, C.E.
History
DepositionApr 1, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)84,13113
Polymers79,8591
Non-polymers4,27212
Water11,638646
1
A: Glutamate carboxypeptidase 2
hetero molecules

A: Glutamate carboxypeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,26226
Polymers159,7182
Non-polymers8,54424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area13830 Å2
ΔGint69 kcal/mol
Surface area49990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.625, 130.326, 158.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / PSM / PSMA / Pteroylpoly-gamma-glutamate carboxypeptidase


Mass: 79859.031 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 44-750
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOLH, FOLH1, GIG27, NAALAD1, PSM, PSMA / Cell (production host): S2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q04609, glutamate carboxypeptidase II

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Sugars , 5 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.: 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
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: 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
#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
#9: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


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

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Non-polymers , 5 types, 651 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
#10: Chemical ChemComp-T57 / N-{6-[(4-fluorobenzoyl)amino]hexanoyl}-L-gamma-glutamyl-5-{[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]oxy}-L-norvaline


Mass: 706.608 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H40FN4O14P
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 3.31 Å3/Da / Density % sol: 62.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 33% (v/v) pentaerythritol propoxylate PO/OH 5/4, 0.5 % (w/v) PEG 3350, 100mM Tris-HCl, pH 8.0 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 25, 2012
RadiationMonochromator: KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 110214 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3

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Processing

Software
NameClassification
MAR345dtbdata collection
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.73→19.71 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.882 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18069 5511 5 %RANDOM
Rwork0.15824 ---
obs0.15937 104702 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.906 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.73→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5529 0 274 646 6449
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0226311
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6452.018584
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9515725
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.90823.958288
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.188151029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1861534
X-RAY DIFFRACTIONr_chiral_restr0.1240.2931
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214816
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8541.53596
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.40325867
X-RAY DIFFRACTIONr_scbond_it2.40432715
X-RAY DIFFRACTIONr_scangle_it3.7944.52717
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.726→1.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 371 -
Rwork0.274 7051 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 17.7529 Å / Origin y: 49.7382 Å / Origin z: 44.4061 Å
111213212223313233
T0.0126 Å20.012 Å20.0046 Å2-0.0454 Å2-0.0176 Å2--0.0371 Å2
L0.5045 °2-0.2624 °20.0094 °2-0.9337 °20.0533 °2--0.3351 °2
S-0.0568 Å °0.0208 Å °-0.027 Å °0.0171 Å °0.0524 Å °-0.1487 Å °0.0256 Å °0.0624 Å °0.0044 Å °

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