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- PDB-5lg6: Structure of the deglycosylated porcine aminopeptidase N ectodomain -

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Basic information

Entry
Database: PDB / ID: 5lg6
TitleStructure of the deglycosylated porcine aminopeptidase N ectodomain
ComponentsAminopeptidase N
KeywordsHYDROLASE / CD13 / pAPN / porcine aminopeptidase N / Coronavirus
Function / homology
Function and homology information


membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / cell differentiation / proteolysis / extracellular space / zinc ion binding ...membrane alanyl aminopeptidase / peptide catabolic process / metalloaminopeptidase activity / peptide binding / virus receptor activity / angiogenesis / cell differentiation / proteolysis / extracellular space / zinc ion binding / plasma membrane / cytoplasm
Similarity search - Function
Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Zincin-like fold / tricorn interacting facor f3 domain / Aminopeptidase N-like , N-terminal domain / Peptidase M1, alanine aminopeptidase/leukotriene A4 hydrolase / Peptidase M1, membrane alanine aminopeptidase ...Zincin-like fold - #20 / Immunoglobulin-like - #1910 / Aminopeptidase N-type / ERAP1-like C-terminal domain / ERAP1-like C-terminal domain / Zincin-like fold / tricorn interacting facor f3 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 / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Alpha Horseshoe / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSantiago, C. / Reguera, J. / Mudgal, G. / Casasnovas, J.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of ScienceBFU2011-23940 and BIO2014-52683-R Spain
CitationJournal: Sci Rep / Year: 2017
Title: Allosteric inhibition of aminopeptidase N functions related to tumor growth and virus infection.
Authors: Santiago, C. / Mudgal, G. / Reguera, J. / Recacha, R. / Albrecht, S. / Enjuanes, L. / Casasnovas, J.M.
History
DepositionJul 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aminopeptidase N
B: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,41222
Polymers222,3002
Non-polymers4,11320
Water6,864381
1
A: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,20611
Polymers111,1501
Non-polymers2,05610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,20611
Polymers111,1501
Non-polymers2,05610
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.465, 215.690, 78.630
Angle α, β, γ (deg.)90.000, 91.900, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 61:126 or resseq 131:138 or resseq...
21chain B and (resseq 61:126 or resseq 131:138 or resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 61:126 or resseq 131:138 or resseq...A61 - 126
121chain A and (resseq 61:126 or resseq 131:138 or resseq...A131 - 138
131chain A and (resseq 61:126 or resseq 131:138 or resseq...A141 - 564
141chain A and (resseq 61:126 or resseq 131:138 or resseq...A575 - 888
151chain A and (resseq 61:126 or resseq 131:138 or resseq...A894 - 963
211chain B and (resseq 61:126 or resseq 131:138 or resseq...B61 - 126
221chain B and (resseq 61:126 or resseq 131:138 or resseq...B131 - 138
231chain B and (resseq 61:126 or resseq 131:138 or resseq...B141 - 564
241chain B and (resseq 61:126 or resseq 131:138 or resseq...B575 - 888
251chain B and (resseq 61:126 or resseq 131:138 or resseq...B894 - 963

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Components

#1: Protein Aminopeptidase N / pAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / gp130


Mass: 111149.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ANPEP / Cell line (production host): CHO LEC 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P15145, membrane alanyl aminopeptidase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Source: (gene. exp.) Sus scrofa (pig) / Cell line (production host): CHO LEC 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster)
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
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 5% PEG-1000, 10% PEG-8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 8, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 73869 / % possible obs: 97 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 6
Reflection shellResolution: 2.5→2.589 Å

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Processing

Software
NameVersionClassification
PHENIX1.7.1_743refinement
XDSdata reduction
SCALAdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→24.982 Å / FOM work R set: 0.8562 / SU ML: 0.58 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2294 2000 2.71 %
Rwork0.1908 71863 -
obs0.1918 73863 97.03 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 8.496 Å2 / ksol: 0.293 e/Å3
Displacement parametersBiso max: 192.46 Å2 / Biso mean: 19.93 Å2 / Biso min: 2.75 Å2
Baniso -1Baniso -2Baniso -3
1-6.7311 Å2-0 Å2-1.4465 Å2
2---2.0942 Å2-0 Å2
3----4.637 Å2
Refinement stepCycle: final / Resolution: 2.5→24.982 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14292 0 254 381 14927
Biso mean--37.67 20.42 -
Num. residues----1776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00914933
X-RAY DIFFRACTIONf_angle_d1.26620315
X-RAY DIFFRACTIONf_chiral_restr0.0972273
X-RAY DIFFRACTIONf_plane_restr0.0062592
X-RAY DIFFRACTIONf_dihedral_angle_d17.5975426
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A7104X-RAY DIFFRACTIONPOSITIONAL0.062
12B7104X-RAY DIFFRACTIONPOSITIONAL0.062
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.56250.29031460.23685076522296
2.5625-2.63170.26631270.21795019514695
2.6317-2.7090.25631510.2155042519396
2.709-2.79640.26831430.21265090523396
2.7964-2.89620.2651450.21865107525296
2.8962-3.01190.27051390.21715101524097
3.0119-3.14880.26281350.20775137527297
3.1488-3.31440.2441470.19775139528698
3.3144-3.52150.20351430.17785186532998
3.5215-3.79260.19061460.175139528598
3.7926-4.17270.21241420.16725249539198
4.1727-4.77280.19341520.15165162531498
4.7728-5.99940.19091440.17155160530497
5.9994-24.98330.22231400.19645256539698

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