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- PDB-5bpk: Varying binding modes of inhibitors and structural differences in... -

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Basic information

Entry
Database: PDB / ID: 5bpk
TitleVarying binding modes of inhibitors and structural differences in the binding pockets of different gamma-glutamyltranspeptidases
Components(Gamma-glutamyltranspeptidase (Ggt)) x 2
KeywordsHYDROLASE / gamma-GLUTAMYLTRANSPEPTIDASE / NTN-HYDROLASE / Acivicin / PROTEROS BIOSTRUCTURES GMBH
Function / homology
Function and homology information


gamma-glutamyltransferase / glutathione gamma-glutamate hydrolase / glutathione hydrolase activity / leukotriene C4 gamma-glutamyl transferase activity / glutathione catabolic process / negative regulation of cell cycle G1/S phase transition / glutathione biosynthetic process / negative regulation of T cell proliferation / positive regulation of interleukin-8 production
Similarity search - Function
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 / Nucleophile aminohydrolases, N-terminal / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-4UD / Glutathione hydrolase proenzyme
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
Helicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 Å
AuthorsBolz, C. / Bach, N.C. / Meyer, H. / Mueller, G. / Dawidowski, M. / Popowicz, G. / Sieber, S.A. / Skerra, A. / Gerhard, M.
CitationJournal: To Be Published
Title: Varying binding modes of inhibitors and structural differences in the binding pockets of different gamma-glutamyltranspeptidases
Authors: Bolz, C. / Bach, N.C. / Meyer, H. / Mueller, G. / Dawidowski, M. / Popowicz, G. / Sieber, S.A. / Skerra, A. / Gerhard, M.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _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 (Ggt)
C: Gamma-glutamyltranspeptidase (Ggt)
B: Gamma-glutamyltranspeptidase (Ggt)
D: Gamma-glutamyltranspeptidase (Ggt)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,73749
Polymers130,7794
Non-polymers2,95745
Water17,258958
1
A: Gamma-glutamyltranspeptidase (Ggt)
C: Gamma-glutamyltranspeptidase (Ggt)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,77523
Polymers65,3902
Non-polymers1,38521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15670 Å2
ΔGint-12 kcal/mol
Surface area20530 Å2
MethodPISA
2
B: Gamma-glutamyltranspeptidase (Ggt)
D: Gamma-glutamyltranspeptidase (Ggt)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,96126
Polymers65,3902
Non-polymers1,57224
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14240 Å2
ΔGint-29 kcal/mol
Surface area20640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.777, 112.006, 91.854
Angle α, β, γ (deg.)90.000, 90.790, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Gamma-glutamyltranspeptidase (Ggt)


Mass: 40832.039 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, residues 1-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: HP_1118 / Production host: Escherichia coli (E. coli) / References: UniProt: O25743
#2: Protein Gamma-glutamyltranspeptidase (Ggt)


Mass: 24557.641 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, residues 380-567
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: / 26695 / Gene: HP_1118 / Production host: Escherichia coli (E. coli) / References: UniProt: O25743
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 43 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-4UD / (2S)-amino[(5S)-4,5-dihydro-1,2-oxazol-5-yl]acetic acid


Type: L-peptide linking / Mass: 144.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H8N2O3 / Source: (gene. exp.) Helicobacter pylori (bacteria) / Production host: Escherichia coli (E. coli)
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 958 / 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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG3350, 0.1M TRIS

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→91.84 Å / Num. obs: 176874 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.6
Reflection shellResolution: 1.49→1.55 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.51 / Rejects: 0 / % possible all: 98.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.5.0088refinement
MOLREPphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NQO

2nqo


Resolution: 1.49→91.8 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.592 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1837 4718 2.7 %RANDOM
Rwork0.1438 ---
obs0.1449 170766 99.21 %-
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 max: 57.14 Å2 / Biso mean: 13.238 Å2 / Biso min: 4.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20.53 Å2
2--0.84 Å20 Å2
3----0.33 Å2
Refinement stepCycle: final / Resolution: 1.49→91.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8142 0 192 961 9295
Biso mean--31.62 28.36 -
Num. residues----1072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0228609
X-RAY DIFFRACTIONr_bond_other_d0.0010.025946
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.98111576
X-RAY DIFFRACTIONr_angle_other_deg0.871314601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19251101
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.07825.195333
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.107151486
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7681529
X-RAY DIFFRACTIONr_chiral_restr0.0710.21286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0219501
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021582
X-RAY DIFFRACTIONr_mcbond_it2.28925418
X-RAY DIFFRACTIONr_mcbond_other1.21122223
X-RAY DIFFRACTIONr_mcangle_it3.11438717
X-RAY DIFFRACTIONr_scbond_it4.21943191
X-RAY DIFFRACTIONr_scangle_it5.76662859
X-RAY DIFFRACTIONr_rigid_bond_restr2.009314555
X-RAY DIFFRACTIONr_sphericity_free8.9613961
X-RAY DIFFRACTIONr_sphericity_bonded4.463314423
LS refinement shellResolution: 1.49→1.529 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 363 -
Rwork0.208 12465 -
all-12828 -
obs--98.4 %

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