[English] 日本語
Yorodumi
- PDB-6xpb: Structure of human GGT1 in complex with 2-amino-4-(((1-((carboxym... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xpb
TitleStructure of human GGT1 in complex with 2-amino-4-(((1-((carboxymethyl)amino)-1-oxobutan-2-yl)oxy)(phenoxy)phosphoryl)butanoic acid (ACPB) molecule
Components(Glutathione hydrolase 1 ...) x 2
KeywordsHYDROLASE / Inhibitor-ENZYME COMPLEX / 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 / Gamma-glutamyltranspeptidase signature. / Gamma-glutamyltranspeptidase / Gamma-glutamyltranspeptidase, large subunit, C-terminal domain / Gamma-glutamyltranspeptidase, small subunit / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Chem-V7D / Glutathione hydrolase 1 proenzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.74 Å
AuthorsTerzyan, S.S. / Hanigan, M.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM125952 United States
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Crystal structures of glutathione- and inhibitor-bound human GGT1: critical interactions within the cysteinylglycine binding site.
Authors: Terzyan, S.S. / Nguyen, L.T. / Burgett, A.W.G. / Heroux, A. / Smith, C.A. / You, Y. / Hanigan, M.H.
History
DepositionJul 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 21, 2021Group: Advisory / Database references ...Advisory / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Oct 18, 2023Group: 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 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutathione hydrolase 1 heavy chain
B: Glutathione hydrolase 1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,37112
Polymers58,5482
Non-polymers1,82210
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14780 Å2
ΔGint-93 kcal/mol
Surface area19310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.362, 124.218, 104.232
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-891-

HOH

21A-989-

HOH

31A-1072-

HOH

-
Components

-
Glutathione hydrolase 1 ... , 2 types, 2 molecules AB

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


Mass: 38533.664 Da / Num. of mol.: 1 / Mutation: V272A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGT1, GGT / Plasmid: PPICZAA / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33
References: UniProt: P19440, glutathione gamma-glutamate hydrolase, gamma-glutamyltransferase, leukotriene-C4 hydrolase
#2: Protein Glutathione hydrolase 1 light chain / GGT 1 / Gamma-glutamyltransferase 1 / Glutathione hydrolase 1 / Leukotriene-C4 hydrolase


Mass: 20014.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GGT1, GGT / Plasmid: PPICZAA / Production host: Komagataella pastoris (fungus)
References: UniProt: P19440, glutathione gamma-glutamate hydrolase, gamma-glutamyltransferase, leukotriene-C4 hydrolase

-
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

-
Non-polymers , 4 types, 648 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-V7D / 2,2-diamino-4-[(S)-({(2S)-1-[(carboxymethyl)amino]-1-oxobutan-2-yl}oxy)(hydroxy)phosphanyl]butanoic acid


Mass: 401.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H24N3O7P / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 644 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.06 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 20-25% PEG3350, 0.1M ammonium chloride, 0.1M sodium cacodilate pH6.0
Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 16, 2014 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.74→64 Å / Num. obs: 69800 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15.7
Reflection shellResolution: 1.74→1.77 Å / Redundancy: 5 % / Rmerge(I) obs: 0.64 / Num. unique obs: 3284 / % possible all: 93.6

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4GDX

4gdx


Resolution: 1.74→47.37 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.995 / SU ML: 0.063 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1889 3533 5.1 %RANDOM
Rwork0.1532 ---
obs0.155 66262 98.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 81.88 Å2 / Biso mean: 24.432 Å2 / Biso min: 10.91 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 1.74→47.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4045 0 108 647 4800
Biso mean--39.27 40.56 -
Num. residues----531
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194450
X-RAY DIFFRACTIONr_angle_refined_deg1.6081.9816094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7285591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.12423.351191
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.62715720
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5551537
X-RAY DIFFRACTIONr_chiral_restr0.1150.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213402
LS refinement shellResolution: 1.74→1.783 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.314 243 -
Rwork0.304 4604 -
obs--93.34 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more