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- PDB-7pfs: Crystal structure of ERAP2 aminopeptidase in complex with phosphi... -

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Basic information

Entry
Database: PDB / ID: 7pfs
TitleCrystal structure of ERAP2 aminopeptidase in complex with phosphinic pseudotripeptide ((1R)-1-Amino-3-phenylpropyl){2-([1,1:3,1-terphenyl]-5-ylmethyl)-3-[((2S)-1-amino-1-oxo-3-phenylpropan-2-yl)-amino]-3-oxopropyl}phosphinic acid
ComponentsEndoplasmic reticulum aminopeptidase 2
KeywordsHYDROLASE / ERAP2 / transition state analogues / antigen presentation / phosphinic pseudotripeptides / aminopeptidase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / 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 / antigen processing and presentation of peptide antigen via MHC class I / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide binding / 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 / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase / 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
Chem-7OO / IMIDAZOLE / Endoplasmic reticulum aminopeptidase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGiastas, P. / Stratikos, E. / Mpakali, A.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Union (EU)European Union
CitationJournal: Acs Med.Chem.Lett. / Year: 2022
Title: Inhibitor-Dependent Usage of the S1' Specificity Pocket of ER Aminopeptidase 2.
Authors: Mpakali, A. / Georgiadis, D. / Stratikos, E. / Giastas, P.
History
DepositionAug 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)230,22127
Polymers222,0222
Non-polymers8,20025
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint101 kcal/mol
Surface area74140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.135, 133.822, 128.703
Angle α, β, γ (deg.)90.000, 90.285, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 111010.820 Da / Num. of mol.: 2 / Mutation: K392N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERAP2, LRAP / Production host: Trichoplusia ni (cabbage looper)
References: UniProt: Q6P179, Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases

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Sugars , 4 types, 17 molecules

#2: 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.: 3
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
#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.: 5
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 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
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8 / 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 , 5 types, 88 molecules

#6: Chemical ChemComp-7OO / [(2~{S})-3-[[(2~{S})-1-azanyl-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-2-[(3,5-diphenylphenyl)methyl]-3-oxidanylidene-propyl]-[(1~{R})-1-azanyl-3-phenyl-propyl]phosphinic acid


Mass: 625.737 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H44N3O4P / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#9: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.92 Å3/Da / Density % sol: 57.86 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% w/v PEG 8000, 20% v/v ethylene glycol, 0.02M of each monosaccharide (0.2M D-glucose, 0.2M D-mannose, 0.2M D-galactose,0.2M L-fucose, 0.2M D-xylose, 0.2M N-acetyl-D-glucosamine), 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: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.7→65.03 Å / Num. obs: 61923 / % possible obs: 88.6 % / Redundancy: 2 % / Biso Wilson estimate: 65.41 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.0441 / Rpim(I) all: 0.0441 / Net I/σ(I): 10.76
Reflection shellResolution: 2.7→2.797 Å / Mean I/σ(I) obs: 1.72 / Num. unique obs: 3318 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
PHENIX1.14_3219refinement
PHENIX1.14_3219refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AB0

5ab0


Resolution: 2.7→65.03 Å / SU ML: 0.4013 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.1083 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2384 3101 5.01 %
Rwork0.1882 58816 -
obs0.1908 61917 88.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→65.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14145 0 537 80 14762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011515098
X-RAY DIFFRACTIONf_angle_d1.40820571
X-RAY DIFFRACTIONf_chiral_restr0.07872373
X-RAY DIFFRACTIONf_plane_restr0.00822549
X-RAY DIFFRACTIONf_dihedral_angle_d6.14212087
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.740.3833730.2951275X-RAY DIFFRACTION42.66
2.74-2.790.3324730.2771541X-RAY DIFFRACTION50.71
2.79-2.840.373890.28381727X-RAY DIFFRACTION58.32
2.84-2.890.34511140.26171949X-RAY DIFFRACTION64.87
2.89-2.940.30871040.25352236X-RAY DIFFRACTION73.77
2.94-30.34391330.26542587X-RAY DIFFRACTION85.4
3-3.070.2971350.26862815X-RAY DIFFRACTION94.58
3.07-3.140.33351590.27043014X-RAY DIFFRACTION99.47
3.14-3.220.3621890.26672960X-RAY DIFFRACTION100
3.22-3.30.35141390.25813022X-RAY DIFFRACTION99.72
3.3-3.40.22661460.21533074X-RAY DIFFRACTION99.97
3.4-3.510.3051940.21952670X-RAY DIFFRACTION88.56
3.51-3.640.25981680.1943001X-RAY DIFFRACTION99.97
3.64-3.780.23241750.18463014X-RAY DIFFRACTION99.75
3.78-3.950.24331320.18592823X-RAY DIFFRACTION93.28
3.95-4.160.22681540.16053020X-RAY DIFFRACTION99.78
4.16-4.420.20311740.1532992X-RAY DIFFRACTION99.72
4.42-4.770.18321680.14032997X-RAY DIFFRACTION99.53
4.77-5.240.20422050.14542949X-RAY DIFFRACTION99.9
5.24-60.23921580.17263037X-RAY DIFFRACTION99.66
6-7.560.22741640.19293031X-RAY DIFFRACTION99.47
7.56-7.56510.19561550.1663082X-RAY DIFFRACTION99.17
Refinement TLS params.Method: refined / Origin x: 19.1468887638 Å / Origin y: 3.06791744566 Å / Origin z: 30.3394671441 Å
111213212223313233
T0.206147845954 Å2-0.0521105621122 Å20.00766161523437 Å2-0.245437899083 Å20.0598554993857 Å2--0.360784811692 Å2
L0.519043757447 °2-0.0510347006909 °20.0249535081074 °2-0.865011894584 °20.1198854811 °2--1.02636581562 °2
S0.0814396613376 Å °-0.0994707331123 Å °-0.105497824369 Å °0.145357555942 Å °-0.00837406045225 Å °0.164384426316 Å °0.00368073827677 Å °-0.0944640662564 Å °-0.0622748623425 Å °
Refinement TLS groupSelection details: all

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