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- PDB-6gbx: Crystal structure of human glutaminyl cyclase variant Y115E-Y117E... -

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Basic information

Entry
Database: PDB / ID: 6gbx
TitleCrystal structure of human glutaminyl cyclase variant Y115E-Y117E in complex with SEN177
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / Inhibitor / Cyclotransferase / zinc enzyme / Alzheimer
Function / homology
Function and homology information


peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / protein modification process / specific granule lumen / tertiary granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / zinc ion binding / extracellular region
Similarity search - Function
M28 Zn-Peptidase Glutaminyl Cyclase / Glutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-S77 / Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsPozzi, C. / Di Pisa, F. / Benvenuti, M. / Mangani, S.
CitationJournal: J. Biol. Inorg. Chem. / Year: 2018
Title: The structure of the human glutaminyl cyclase-SEN177 complex indicates routes for developing new potent inhibitors as possible agents for the treatment of neurological disorders.
Authors: Pozzi, C. / Di Pisa, F. / Benvenuti, M. / Mangani, S.
History
DepositionApr 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 19, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutaminyl-peptide cyclotransferase
B: Glutaminyl-peptide cyclotransferase
C: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,20932
Polymers112,4683
Non-polymers2,74129
Water12,556697
1
A: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2999
Polymers37,4891
Non-polymers8108
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,54813
Polymers37,4891
Non-polymers1,05812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,36210
Polymers37,4891
Non-polymers8729
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.140, 149.810, 95.980
Angle α, β, γ (deg.)90.00, 97.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-539-

HOH

21A-713-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Glutaminyl-peptide cyclotransferase / / Glutaminyl cyclase / sQC / Glutaminyl-tRNA cyclotransferase / Glutamyl cyclase / EC


Mass: 37489.277 Da / Num. of mol.: 3 / Mutation: Y115E; Y117E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q16769, glutaminyl-peptide cyclotransferase

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Non-polymers , 5 types, 726 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-S77 / 2-fluoranyl-5-[2-[4-(4-methyl-1,2,4-triazol-3-yl)piperidin-1-yl]pyridin-3-yl]pyridine


Mass: 338.382 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H19FN6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 697 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, 0.4 M ammonium sulfate, 0.07 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.72→95.23 Å / Num. obs: 126884 / % possible obs: 99.8 % / Redundancy: 3.4 % / Biso Wilson estimate: 9.28 Å2 / CC1/2: 0.985 / Rrim(I) all: 0.13 / Net I/σ(I): 5.3
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 6232 / CC1/2: 0.567 / Rrim(I) all: 0.75 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4yu9

4yu9


Resolution: 1.72→95.23 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.126 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.087 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18307 6549 5.2 %RANDOM
Rwork0.15819 ---
obs0.15948 120334 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.516 Å2
Refinement stepCycle: 1 / Resolution: 1.72→95.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7841 0 173 697 8711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0158311
X-RAY DIFFRACTIONr_bond_other_d0.0020.0177264
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.76311295
X-RAY DIFFRACTIONr_angle_other_deg0.6231.71817047
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.63151004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.7419.697330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.677151133
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9761550
X-RAY DIFFRACTIONr_chiral_restr0.150.21041
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0219307
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021547
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_it1.6321.4753963
X-RAY DIFFRACTIONr_mcbond_other1.6311.4753964
X-RAY DIFFRACTIONr_mcangle_it2.7032.2044957
X-RAY DIFFRACTIONr_mcangle_other2.7032.2044958
X-RAY DIFFRACTIONr_scbond_it2.4191.6684348
X-RAY DIFFRACTIONr_scbond_other2.4181.6684348
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7412.4076329
X-RAY DIFFRACTIONr_long_range_B_refined4.93818.0099148
X-RAY DIFFRACTIONr_long_range_B_other4.93518.0089148
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.722→1.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 464 -
Rwork0.248 8860 -
obs--99.41 %

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