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- PDB-4zcg: Crystal Structure of human GGT1 in complex with Glutamate (with a... -

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Basic information

Entry
Database: PDB / ID: 4zcg
TitleCrystal Structure of human GGT1 in complex with Glutamate (with all atoms of glutamate)
Components(Gamma-glutamyltranspeptidase 1 ...) x 2
KeywordsHYDROLASE / NTN-HYDROLASE FAMILY / GLYCOPROTEIN / N- GLYCOSYLATION / CELL SURFACE
Function / homology
Function and homology information


leukotriene-C4 hydrolase / peptidyltransferase activity / leukotriene-C(4) hydrolase / leukotriene D4 biosynthetic process / Defective GGT1 causes GLUTH / Defective GGT1 in aflatoxin detoxification causes GLUTH / Glutathione synthesis and recycling / LTC4-CYSLTR mediated IL4 production / gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase ...leukotriene-C4 hydrolase / peptidyltransferase activity / leukotriene-C(4) hydrolase / leukotriene D4 biosynthetic process / Defective GGT1 causes GLUTH / Defective GGT1 in aflatoxin detoxification causes GLUTH / Glutathione synthesis and recycling / LTC4-CYSLTR mediated IL4 production / gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / peptide modification / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / glutamate metabolic process / glutathione biosynthetic process / leukotriene metabolic process / cysteine biosynthetic process / Aflatoxin activation and detoxification / Synthesis of Leukotrienes (LT) and Eoxins (EX) / Paracetamol ADME / amino acid metabolic process / regulation of immune system process / zymogen activation / fatty acid metabolic process / regulation of inflammatory response / spermatogenesis / proteolysis / extracellular space / extracellular exosome / plasma membrane
Similarity search - Function
Gamma-glutamyltranspeptidase, small (S) subunit / Gamma-glutamyltranspeptidase, large (L) subunit, C-terminal domain / : / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Serum Albumin; Chain A, Domain 1 / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 ...Gamma-glutamyltranspeptidase, small (S) subunit / Gamma-glutamyltranspeptidase, large (L) subunit, C-terminal domain / : / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Serum Albumin; Chain A, Domain 1 / Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 / Nucleophile aminohydrolases, N-terminal / 4-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GLUTAMIC ACID / Glutathione hydrolase 1 proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.22 Å
Model detailsComplex
AuthorsTerzyan, S. / Hanigan, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103640 United States
Citation
Journal: J.Biol.Chem. / Year: 2015
Title: Human gamma-Glutamyl Transpeptidase 1: STRUCTURES OF THE FREE ENZYME, INHIBITOR-BOUND TETRAHEDRAL TRANSITION STATES, AND GLUTAMATE-BOUND ENZYME REVEAL NOVEL MOVEMENT WITHIN THE ACTIVE SITE DURING CATALYSIS.
Authors: Terzyan, S.S. / Burgett, A.W. / Heroux, A. / Smith, C.A. / Mooers, B.H. / Hanigan, M.H.
#1: Journal: J.Biol. Chem / Year: 2014
Title: Novel insights into eukaryotic gamma-glutamyl transpeptidase 1 from the crystal structure of the glutamate-bound human enzyme.
Authors: West, M. / Chen, Y. / Wickham, S. / Heroux, A. / Cahill, K. / Hanigan, M. / Mooers, B.
History
DepositionApr 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jul 29, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Database references / Category: pdbx_audit_support / struct_ref_seq_dif
Item: _pdbx_audit_support.funding_organization / _struct_ref_seq_dif.details
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_radiation_wavelength ...chem_comp / diffrn_radiation_wavelength / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-glutamyltranspeptidase 1 heavy chain
B: Gamma-glutamyltranspeptidase 1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,11612
Polymers58,5482
Non-polymers1,56810
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14540 Å2
ΔGint-92 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.242, 125.230, 104.061
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-948-

HOH

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Components

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Gamma-glutamyltranspeptidase 1 ... , 2 types, 2 molecules AB

#1: Protein Gamma-glutamyltranspeptidase 1 heavy chain / GGT 1 / Gamma-glutamyltransferase 1 / Glutathione hydrolase 1 / Leukotriene-C4 hydrolase


Mass: 38533.664 Da / Num. of mol.: 1 / Fragment: Large subunit RESIDUES 28-380
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGT1, GGT / Plasmid: pPICZaA / Production host: PICHIA (fungus) / Strain (production host): X-33
References: UniProt: P19440, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase, leukotriene-C4 hydrolase
#2: Protein Gamma-glutamyltranspeptidase 1 light chain / GGT 1 / Gamma-glutamyltransferase 1 / Glutathione hydrolase 1 / Leukotriene-C4 hydrolase


Mass: 20014.438 Da / Num. of mol.: 1 / Fragment: Small subunit RESIDUES 381-569
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGT1, GGT / Plasmid: pPICZaA / Production host: PICHIA (fungus) / Strain (production host): X-33
References: UniProt: P19440, gamma-glutamyltransferase, glutathione gamma-glutamate hydrolase, leukotriene-C4 hydrolase

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Sugars , 1 types, 6 molecules

#3: 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.: 6
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 , 4 types, 432 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG3350, NH4Cl / PH range: 6.0-6.3 / Temp details: Room Temperature

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2013 / Details: mirrors
RadiationMonochromator: Si 111 doble crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 37862 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 23.09 Å2 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.029 / Rrim(I) all: 0.1 / Χ2: 1.048 / Net I/av σ(I): 21.923 / Net I/σ(I): 9.6 / Num. measured all: 391920
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.142.60.45210460.7990.2910.5421.04152.4
2.14-2.183.20.46612890.8040.2720.5440.97663.9
2.18-2.224.10.4414560.8620.2310.51.0271.7
2.22-2.264.80.42116610.8780.2030.4711.04283.7
2.26-2.315.80.38918080.9060.1720.4281.06290
2.31-2.376.90.36319500.9250.1470.3941.08596.2
2.37-2.428.40.31920120.9590.1150.341.05199.5
2.42-2.4910.30.30820090.9750.1010.3240.998100
2.49-2.5611.30.26120190.980.0810.2741.031100
2.56-2.6512.90.22720360.9880.0650.2361.022100
2.65-2.7412.80.18620200.990.0540.1941.053100
2.74-2.8512.50.16220190.9920.0480.1691.068100
2.85-2.9812.90.13820200.9940.040.1441.073100
2.98-3.1412.80.11920400.9960.0340.1241.077100
3.14-3.3312.80.09820410.9970.0280.1021.079100
3.33-3.5912.60.08320510.9970.0240.0861.09100
3.59-3.9512.70.06820370.9980.020.0711.082100
3.95-4.5212.60.0620860.9970.0180.0630.999100
4.52-5.712.80.05920830.9990.0170.0621.017100
5.7-5012.10.05521790.9990.0160.0581.012100

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
REFMAC5.8.0073phasing
HKL-2000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4GDX

4gdx


Resolution: 2.22→40.02 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.303 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.194 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1852 1704 5 %RANDOM
Rwork0.1463 ---
obs0.1483 32064 98.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.42 Å2 / Biso mean: 35.053 Å2 / Biso min: 17.7 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0.03 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.22→40.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 97 428 4571
Biso mean--61.94 44.77 -
Num. residues----531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194290
X-RAY DIFFRACTIONr_bond_other_d0.0010.024082
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9765850
X-RAY DIFFRACTIONr_angle_other_deg0.77839351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9485550
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17223.69187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23115684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6561532
X-RAY DIFFRACTIONr_chiral_restr0.0780.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214905
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02981
X-RAY DIFFRACTIONr_mcbond_it2.1133.1822147
X-RAY DIFFRACTIONr_mcbond_other2.1123.1822146
X-RAY DIFFRACTIONr_mcangle_it3.3624.7622684
LS refinement shellResolution: 2.22→2.278 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 114 -
Rwork0.239 2046 -
all-2160 -
obs--85.48 %

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