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- PDB-9gjn: ERAP1 in complex with 1-[2-(3-oxo-3,4-dihydro-2H-1,4-benzothiazin... -

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Basic information

Entry
Database: PDB / ID: 9gjn
TitleERAP1 in complex with 1-[2-(3-oxo-3,4-dihydro-2H-1,4-benzothiazin-4-yl)acetamido]cyclohexane-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
: / BROMIDE ION / Endoplasmic reticulum aminopeptidase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.717 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

Downloads & links

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Assembly

Deposited unit
A: Endoplasmic reticulum aminopeptidase 1
B: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,22325
Polymers210,6872
Non-polymers2,53723
Water31,6341756
1
A: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,93617
Polymers105,3431
Non-polymers1,59216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmic reticulum aminopeptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,2888
Polymers105,3431
Non-polymers9447
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.544, 145.430, 112.853
Angle α, β, γ (deg.)90.00, 93.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#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: 105343.398 Da / Num. of mol.: 2
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 , 6 types, 1779 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#6: Chemical ChemComp-A1IMK / 1-[2-(3-oxidanylidene-1,4-benzothiazin-4-yl)ethanoylamino]cyclohexane-1-carboxylic acid / 1-[2-(3-oxo-3,4-dihydro-2H-1,4-benzothiazin-4-yl)acetamido]cyclohexane-1-carboxylic acid


Mass: 348.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N2O4S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1756 / 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: 2.24 Å3/Da / Density % sol: 45.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NaBr, 20% w/v PEG 3350, 0.1 M Bis-Tris propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.71→113 Å / Num. obs: 149277 / % possible obs: 75.9 % / Redundancy: 3 % / CC1/2: 0.996 / Net I/σ(I): 1.6
Reflection shellResolution: 1.72→1.79 Å / Num. unique obs: 7466 / CC1/2: 0.559

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (26-JUL-2023)refinement
autoPROCdata reduction
autoPROCdata scaling
autoBUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.717→112.67 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.144 / SU Rfree Blow DPI: 0.13 / SU Rfree Cruickshank DPI: 0.127
RfactorNum. reflection% reflectionSelection details
Rfree0.208 7364 4.93 %RANDOM
Rwork0.1692 ---
obs0.1711 149277 75.8 %-
Displacement parametersBiso mean: 26.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.6848 Å20 Å2-0.2387 Å2
2---0.796 Å20 Å2
3---1.4809 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.717→112.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13841 0 141 1756 15738
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00914396HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9519508HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5062SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2415HARMONIC5
X-RAY DIFFRACTIONt_it14396HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.61
X-RAY DIFFRACTIONt_other_torsion16.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1855SEMIHARMONIC5
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_contact14168SEMIHARMONIC4
LS refinement shellResolution: 1.72→1.75 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.308 150 5.02 %
Rwork0.2601 2836 -
all0.2625 2986 -
obs--27.71 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.19530.1120.00130.2684-0.06350.09970.00150.02620.01040.004-0.00230.0147-0.01440.00440.0007-0.0368-0.009-0.0006-0.0291-0.00860.0124-10.03833.1752-54.0356
20.0933-0.16610.05010.3632-0.03110.26020.0097-0.02350.01070.0351-0.0151-0.0160.035-0.08040.0054-0.0418-0.0021-0.01050.0048-0.0082-0.034-16.060369.3064-1.4601
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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