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- PDB-4zc6: Crystal Structure of human GGT1 in complex with Serine Borate -

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Basic information

Entry
Database: PDB / ID: 4zc6
TitleCrystal Structure of human GGT1 in complex with Serine Borate
Components(Gamma-glutamyltranspeptidase 1 ...) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / NTN-HYDROLASE FAMILY / GLYCOPROTEIN / N- GLYCOSYLATION / CELL SURFACE / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
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
trihydroxy(L-serinato-kappaO~3~)borate(1-) / Glutathione hydrolase 1 proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
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
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

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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)60,13512
Polymers58,5482
Non-polymers1,58710
Water6,035335
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14550 Å2
ΔGint-90 kcal/mol
Surface area19260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.182, 124.360, 103.613
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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, 339 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-SEE / trihydroxy(L-serinato-kappaO~3~)borate(1-)


Type: L-peptide linking / Mass: 165.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9BNO6
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG3350, NH4Cl / Temp details: ROOM TEMPERATURE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2014 / Details: mirrors
RadiationMonochromator: Si 111 doble crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. obs: 38155 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.063 / Rrim(I) all: 0.166 / Χ2: 1.023 / Net I/av σ(I): 9 / Net I/σ(I): 5.3 / Num. measured all: 241835
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.144.80.63415110.6890.2830.7011.00277
2.14-2.184.80.58915690.7360.2660.6521.04380
2.18-2.225.30.56317090.7510.2450.6191.03686.6
2.22-2.265.90.4918450.7930.2040.5351.04792.9
2.26-2.316.10.48719200.7810.2040.5321.03897
2.31-2.376.30.4419360.8280.1820.481.05198.7
2.37-2.426.50.4419690.830.1860.4821.03499.1
2.42-2.496.60.40319710.8550.1660.4391.01999.5
2.49-2.566.70.36319640.8840.1490.3951.03399.4
2.56-2.656.70.29919750.9290.1220.3261.02398.8
2.65-2.746.40.25619430.9380.1060.281.02798.4
2.74-2.855.90.22119060.9570.0940.2421.02396.1
2.85-2.9870.19819890.9680.0780.2141.03199.5
2.98-3.146.90.1720080.9760.0680.1841.03399.5
3.14-3.336.90.13319500.9840.0520.1441.0399.2
3.33-3.596.80.11320040.9880.0450.1221.03299
3.59-3.956.50.09519630.9910.0380.1031.02797.9
3.95-4.526.40.08119750.9910.0330.0880.98596.8
4.52-5.76.90.07920050.9930.0320.0861.00398.2
5.7-1006.40.06420430.9950.0270.070.9695.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACT3.15data extraction
REFMAC5.8.0073phasing
HKL-2000data reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4Z9O

4z9o


Resolution: 2.1→80.31 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.592 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 1939 5.1 %RANDOM
Rwork0.1746 ---
obs0.1768 36179 95.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.19 Å2 / Biso mean: 28.685 Å2 / Biso min: 11.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å20 Å2
2--0.03 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.1→80.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4046 0 97 335 4478
Biso mean--53.32 36.3 -
Num. residues----531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194290
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.9765842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0985543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24423.548186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59115672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0811533
X-RAY DIFFRACTIONr_chiral_restr0.090.2675
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213284
X-RAY DIFFRACTIONr_mcbond_it1.4992.5552151
X-RAY DIFFRACTIONr_mcangle_it2.4113.8222695
X-RAY DIFFRACTIONr_scbond_it2.8553.0092139
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 113 -
Rwork0.284 2090 -
all-2203 -
obs--75.57 %

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