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- PDB-9gjs: ERAP1 in complex with 1-[2-(6-bromo-3-oxo-3,4-dihydro-2H-1,4-benz... -

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Basic information

Entry
Database: PDB / ID: 9gjs
TitleERAP1 in complex with 1-[2-(6-bromo-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-4-yl)acetamido]-4,4-difluorocyclohexane-1-carboxylic acid
ComponentsEndoplasmic reticulum aminopeptidase 1
KeywordsPEPTIDE BINDING PROTEIN / ERAP1
Function / homology
Function and homology information


interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloexopeptidase activity / regulation of innate immune response / peptide catabolic process / antigen processing and presentation of peptide antigen via MHC class I / fat cell differentiation / metalloaminopeptidase activity / membrane protein ectodomain proteolysis ...interleukin-1, type II receptor binding / interleukin-6 receptor binding / Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / metalloexopeptidase activity / regulation of innate immune response / peptide catabolic process / antigen processing and presentation of peptide antigen via MHC class I / fat cell differentiation / metalloaminopeptidase activity / membrane protein ectodomain proteolysis / aminopeptidase activity / peptide binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to bacterium / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / positive regulation of angiogenesis / angiogenesis / endopeptidase activity / adaptive immune response / endoplasmic reticulum lumen / endoplasmic reticulum membrane / endoplasmic reticulum / proteolysis / extracellular space / extracellular exosome / extracellular region / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy ...Aminopeptidase N-type / ERAP1-like C-terminal domain / : / ERAP1-like C-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / Aminopeptidase N-like , N-terminal domain / Peptidase family M1 domain / Peptidase M1 N-terminal domain / Aminopeptidase N-like , N-terminal domain superfamliy / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
: / PHOSPHATE ION / Endoplasmic reticulum aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.351 Å
AuthorsRowland, P.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Med.Chem.Lett. / Year: 2024
Title: Optimization of Potent and Selective Cyclohexyl Acid ERAP1 Inhibitors Using Structure- and Property-Based Drug Design.
Authors: Hryczanek, R.P. / Hackett, A.S. / Rowland, P. / Chung, C.W. / Convery, M.A. / Holmes, D.S. / Hutchinson, J.P. / Kitchen, S. / Korczynska, J. / Law, R.P. / Lea, J.D. / Liddle, J. / Lonsdale, ...Authors: Hryczanek, R.P. / Hackett, A.S. / Rowland, P. / Chung, C.W. / Convery, M.A. / Holmes, D.S. / Hutchinson, J.P. / Kitchen, S. / Korczynska, J. / Law, R.P. / Lea, J.D. / Liddle, J. / Lonsdale, R. / Neu, M. / Nickels, L. / Phillipou, A. / Rowedder, J.E. / Schneck, J.L. / Scott-Stevens, P. / Sheehan, H. / Tayler, C.L. / Temponeras, I. / Tinworth, C.P. / Walker, A.L. / Wojno-Picon, J. / Young, R.J. / Lindsay, D.M. / Stratikos, E.
History
DepositionAug 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,89412
Polymers105,3711
Non-polymers1,52211
Water18,6821037
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)112.693, 140.804, 57.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endoplasmic reticulum aminopeptidase 1 / ARTS-1 / Adipocyte-derived leucine aminopeptidase / A-LAP / Aminopeptidase PILS / Puromycin- ...ARTS-1 / Adipocyte-derived leucine aminopeptidase / A-LAP / Aminopeptidase PILS / Puromycin-insensitive leucyl-specific aminopeptidase / PILS-AP / Type 1 tumor necrosis factor receptor shedding aminopeptidase regulator


Mass: 105371.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP1, APPILS, ARTS1, KIAA0525, UNQ584/PRO1154 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9NZ08, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Non-polymers , 5 types, 1048 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-A1IMJ / 1-[2-(6-bromanyl-3-oxidanylidene-1,4-benzoxazin-4-yl)ethanoylamino]-4,4-bis(fluoranyl)cyclohexane-1-carboxylic acid / 1-[2-(6-bromo-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-4-yl)acetamido]-4,4-difluorocyclohexane-1-carboxylic acid


Mass: 447.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17BrF2N2O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1037 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 22% w/v PEG 1500, 0.1 M SPG buffer pH 5.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→88 Å / Num. obs: 142076 / % possible obs: 70.7 % / Redundancy: 6.5 % / CC1/2: 0.997 / Net I/σ(I): 9.8
Reflection shellResolution: 1.35→1.47 Å / Num. unique obs: 7104 / CC1/2: 0.327

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Processing

Software
NameVersionClassification
autoPROCdata reduction
XDS(VERSION Jan 31data reduction
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
BUSTER2.11.8 (26-JUL-2023)refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.351→19.38 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.075 / SU Rfree Blow DPI: 0.077 / SU Rfree Cruickshank DPI: 0.073
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 7136 5.03 %RANDOM
Rwork0.1706 ---
obs0.1722 141993 70.7 %-
Displacement parametersBiso mean: 23.52 Å2
Baniso -1Baniso -2Baniso -3
1-0.7482 Å20 Å20 Å2
2---0.4261 Å20 Å2
3----0.3221 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 1.351→19.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6927 0 89 1037 8053
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0117262HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.079862HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2562SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1237HARMONIC5
X-RAY DIFFRACTIONt_it7262HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.15
X-RAY DIFFRACTIONt_other_torsion15.46
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion935SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7752SEMIHARMONIC4
LS refinement shellResolution: 1.351→1.42 Å
RfactorNum. reflection% reflection
Rfree0.3009 131 4.61 %
Rwork0.2676 2709 -
obs--10.53 %
Refinement TLS params.Method: refined / Origin x: 30.743 Å / Origin y: 32.7825 Å / Origin z: 12.3661 Å
111213212223313233
T-0.0148 Å20.0092 Å20.0017 Å2--0.0146 Å20.0126 Å2---0.0234 Å2
L0.1378 °20.0777 °2-0.1153 °2-0.2226 °2-0.1056 °2--0.2522 °2
S-0.0042 Å °-0.0273 Å °-0.0162 Å °-0.0291 Å °-0.0125 Å °0.0029 Å °0.0018 Å °0.0169 Å °0.0167 Å °
Refinement TLS groupSelection details: { A|* }

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