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- PDB-7nup: Endoplasmic reticulum aminopeptidase 2 complexed with a mixed hyd... -

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Basic information

Entry
Database: PDB / ID: 7nup
TitleEndoplasmic reticulum aminopeptidase 2 complexed with a mixed hydroxamic and sulfonyl ligand
ComponentsEndoplasmic reticulum aminopeptidase 2
KeywordsHYDROLASE / Hydroxamic inhibitor / complex / aminopeptidase / Zinc containing enzyme
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / peptide catabolic process / metalloaminopeptidase activity / antigen processing and presentation of peptide antigen via MHC class I / aminopeptidase activity / peptide binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / metallopeptidase activity ...Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / peptide catabolic process / metalloaminopeptidase activity / antigen processing and presentation of peptide antigen via MHC class I / aminopeptidase activity / peptide binding / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / antigen processing and presentation of endogenous peptide antigen via MHC class I / regulation of blood pressure / metallopeptidase activity / endopeptidase activity / adaptive immune response / endoplasmic reticulum lumen / endoplasmic reticulum membrane / proteolysis / extracellular space / zinc ion binding / membrane / 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 / TRIETHYLENE GLYCOL / Chem-USK / Endoplasmic reticulum aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMpakali, A. / Giastas, P. / Stratikos, E.
CitationJournal: To Be Published
Title: Endoplasmic reticulum aminopeptidase 2 complexed with a mixed hydroxamic and sulfonyl ligand
Authors: Mpakali, A. / Giastas, P. / Stratikos, E.
History
DepositionMar 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoplasmic reticulum aminopeptidase 2
B: Endoplasmic reticulum aminopeptidase 2
C: Endoplasmic reticulum aminopeptidase 2
D: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)461,30261
Polymers445,7014
Non-polymers15,60157
Water1,928107
1
A: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,78022
Polymers111,4251
Non-polymers4,35521
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,76015
Polymers111,4251
Non-polymers4,33514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,97112
Polymers111,4251
Non-polymers3,54511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Endoplasmic reticulum aminopeptidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,79112
Polymers111,4251
Non-polymers3,36511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.273, 127.186, 133.412
Angle α, β, γ (deg.)90.920, 90.080, 90.870
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Endoplasmic reticulum aminopeptidase 2 / Leukocyte-derived arginine aminopeptidase / L-RAP


Mass: 111425.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP2, LRAP / Cell line (production host): Sf21
Production host: Spodoptera aff. frugiperda 1 BOLD-2017 (butterflies/moths)
References: UniProt: Q6P179, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Sugars , 5 types, 32 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 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.: 17 / Source method: obtained synthetically / 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

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Non-polymers , 6 types, 132 molecules

#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#8: Chemical
ChemComp-USK / (3~{S})-4-(4-hydroxyphenyl)-~{N}-oxidanyl-3-[5-[[(5-phenylthiophen-2-yl)sulfonylamino]methyl]-1,2,3-triazol-1-yl]butanamide


Mass: 513.589 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C23H23N5O5S2
#9: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#11: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Br
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.04 Å3/Da / Density % sol: 59.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.03M of each halide (sodium fluoride, sodium bromide, sodium iodide), 0.1M MES/imidazole pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→48.664 Å / Num. obs: 73659 / % possible obs: 83.24 % / Redundancy: 3.2 % / CC1/2: 0.921 / Net I/σ(I): 1.6
Reflection shellResolution: 3.1→3.142 Å / Num. unique obs: 1151 / CC1/2: 0.6 / % possible all: 35

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AB0

5ab0


Resolution: 3.1→48.664 Å / SU ML: 0.47 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 28.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2666 3482 4.73 %
Rwork0.1818 70177 -
obs0.1858 73659 83.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 354.84 Å2 / Biso mean: 56.5113 Å2 / Biso min: 1.77 Å2
Refinement stepCycle: final / Resolution: 3.1→48.664 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28861 0 958 107 29926
Biso mean--82.2 35.75 -
Num. residues----3589
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.14250.3619690.2623115135
3.1425-3.18740.4223740.2749153845
3.1874-3.23490.47221080.31174052
3.2349-3.28550.41531250.2892227869
3.2855-3.33930.34531760.2468279082
3.3393-3.39690.3321770.2528300290
3.3969-3.45860.418590.275633857
3.4586-3.52520.33381350.2363290190
3.5252-3.59710.32161340.2155328098
3.5971-3.67530.30151040.2179264678
3.6753-3.76070.27041510.197336198
3.7607-3.85470.30321280.1997333097
3.8547-3.95890.31761170.1877205361
3.9589-4.07540.2951800.1729330399
4.0754-4.20680.251440.1581330598
4.2068-4.35710.24871920.148333399
4.3571-4.53140.21382260.1383326198
4.5314-4.73750.20311390.1385335199
4.7375-4.9870.20871240.1362338299
4.987-5.29910.21731230.1505341099
5.2991-5.70770.30092000.1761329099
5.7077-6.2810.28391570.1942331499
6.281-7.18740.26331410.1933332598
7.1874-9.04590.21581770.1596331798
9.0459-48.6640.20891720.1737317895
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)
11.2006-0.0239-0.01850.5855-0.25821.07840.0594-0.0102-0.102-0.1034-0.03470.09040.0715-0.155-0.02720.2212-0.0393-0.03730.1745-0.05810.212712.86080.5797-11.7232
21.75550.78180.49842.20580.4591.413-0.0491-0.273-0.58260.14290.0057-0.15870.42580.11510.01840.34530.0605-0.02230.31460.11250.410734.7978-19.460111.8379
31.38370.46040.13131.2197-0.50151.6109-0.0063-0.27920.21790.06860.04540.0285-0.04480.0591-0.03140.2464-0.0425-0.02620.3005-0.05630.211730.842112.750414.6021
41.7717-0.1002-0.82480.8065-0.15621.75930.1063-0.11810.1177-0.1051-0.0514-0.0833-0.09830.4345-0.05030.2138-0.052-0.01260.37230.00490.200461.9171-3.940654.8819
52.20510.942-0.88051.9256-0.43211.54420.2108-0.20790.59530.1282-0.03090.167-0.9758-0.2073-0.13020.670.04690.07730.3979-0.17980.513541.390818.727978.484
61.16130.3119-0.26581.45490.4371.91660.0769-0.1299-0.11640.1314-0.02810.0510.2063-0.0719-0.03120.2873-0.0565-0.01850.319-0.01240.196442.7569-14.867381.6918
71.8629-0.68-0.09782.54540.14720.8190.15690.33440.2249-0.4158-0.1525-0.389-0.14780.12950.01810.38620.0570.06830.27760.05790.297628.2481-75.1275-22.3295
81.3795-0.2577-0.10711.70780.15650.87380.3096-0.01390.64170.2711-0.01410.0338-0.2351-0.1607-0.20080.64220.04440.11130.25470.00250.694813.9836-49.5147-8.8997
90.91240.2275-0.27592.4296-0.48411.04250.0721-0.23640.24740.8630.10860.7037-0.4637-0.1208-0.08370.78370.02640.22590.4288-0.04640.56835.7473-66.69477.8264
102.5738-0.4896-0.29952.2226-0.98321.9472-0.00150.3197-0.2615-0.3261-0.00150.30390.1645-0.47720.02130.37340.0423-0.03350.4228-0.08050.270239.2933-54.948444.3093
112.0653-0.00790.81641.5094-0.20221.34580.1974-0.1757-1.0004-0.0539-0.0367-0.12230.49780.298-0.04560.54920.16930.0410.40150.12810.81865.1664-74.150855.4193
121.8211-0.29840.91311.3808-0.3271.4743-0.2453-0.5375-0.23290.33760.1373-0.2189-0.0033-0.02070.10950.50130.1004-0.02370.68610.16390.474171.9804-60.051675.3008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 49 through 500 )A49 - 500
2X-RAY DIFFRACTION2chain 'A' and (resid 501 through 712 )A501 - 712
3X-RAY DIFFRACTION3chain 'A' and (resid 713 through 963 )A713 - 963
4X-RAY DIFFRACTION4chain 'B' and (resid 51 through 500 )B51 - 500
5X-RAY DIFFRACTION5chain 'B' and (resid 501 through 672 )B501 - 672
6X-RAY DIFFRACTION6chain 'B' and (resid 673 through 962 )B673 - 962
7X-RAY DIFFRACTION7chain 'C' and (resid 52 through 385 )C52 - 385
8X-RAY DIFFRACTION8chain 'C' and (resid 386 through 605 )C386 - 605
9X-RAY DIFFRACTION9chain 'C' and (resid 606 through 960 )C606 - 960
10X-RAY DIFFRACTION10chain 'D' and (resid 51 through 271 )D51 - 271
11X-RAY DIFFRACTION11chain 'D' and (resid 272 through 638 )D272 - 638
12X-RAY DIFFRACTION12chain 'D' and (resid 639 through 962 )D639 - 962

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