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- PDB-5lds: Structure of the porcine aminopeptidase N ectodomain -

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Basic information

Entry
Database: PDB / ID: 5lds
TitleStructure of the porcine aminopeptidase N ectodomain
ComponentsAminopeptidase N
KeywordsHYDROLASE / CD13 / pAPN / aminopeptidase / Coronavirus / receptor / enzime
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
ACETATE ION / Aminopeptidase N
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSantiago, C. / Reguera, J. / Mudgal, G. / Casasnovas, J.M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of ScienceBFU2011-23940, 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
DepositionJun 27, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Jun 13, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type
Revision 1.3Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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
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
C: Aminopeptidase N
D: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)440,53343
Polymers429,1574
Non-polymers11,37639
Water89,4444965
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A: Aminopeptidase N
B: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)219,99520
Polymers214,5792
Non-polymers5,41718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Aminopeptidase N
hetero molecules

C: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,53823
Polymers214,5792
Non-polymers5,95921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
3
C: Aminopeptidase N
hetero molecules

D: Aminopeptidase N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,53823
Polymers214,5792
Non-polymers5,95921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Unit cell
Length a, b, c (Å)78.670, 78.770, 223.870
Angle α, β, γ (deg.)99.66, 92.62, 111.33
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
Aminopeptidase N / pAPN / Alanyl aminopeptidase / Aminopeptidase M / AP-M / Microsomal aminopeptidase / gp130


Mass: 107289.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: ANPEP / Cell (production host): CHO LEC 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P15145, membrane alanyl aminopeptidase

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Sugars , 4 types, 31 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D- ...beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-[beta-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpb1-6[DManpb1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Glcp]{[(3+1)][a-D-Idop]{}[(6+1)][a-D-Idop]{[(3+1)][a-D-Idop]{}}}}}}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.: 13
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Cell (production host): CHO LEC 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster)
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-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4) ...beta-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Glcp]{[(3+1)][a-D-Idop]{}}}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Source: (gene. exp.) Sus scrofa (pig) / Cell (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

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Non-polymers , 3 types, 4973 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn / Source: (gene. exp.) Sus scrofa (pig) / Cell (production host): CHO LEC 3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster)
#7: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4965 / 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: 2.88 Å3/Da / Density % sol: 57.26 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 20% PEG-3350 and 100 mM sodium acetate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 322701 / % possible obs: 97.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 8.5

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24.961 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 18.64
RfactorNum. reflection% reflection
Rfree0.2065 16202 5.02 %
Rwork0.1694 --
obs0.1713 322686 97.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→24.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29598 0 16 4965 34579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00830433
X-RAY DIFFRACTIONf_angle_d0.90341353
X-RAY DIFFRACTIONf_dihedral_angle_d14.51811047
X-RAY DIFFRACTIONf_chiral_restr0.0364644
X-RAY DIFFRACTIONf_plane_restr0.0045267
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02270.255290.198410227X-RAY DIFFRACTION97
2.0227-2.04650.24345130.18999945X-RAY DIFFRACTION97
2.0465-2.07140.25255440.190210295X-RAY DIFFRACTION97
2.0714-2.09770.23715320.18639975X-RAY DIFFRACTION97
2.0977-2.12520.22385610.180610266X-RAY DIFFRACTION97
2.1252-2.15430.23215470.175710012X-RAY DIFFRACTION97
2.1543-2.18510.21365090.174410326X-RAY DIFFRACTION97
2.1851-2.21770.23274970.176610107X-RAY DIFFRACTION97
2.2177-2.25230.24095200.171710251X-RAY DIFFRACTION97
2.2523-2.28920.19915180.168310107X-RAY DIFFRACTION97
2.2892-2.32870.21585250.165210251X-RAY DIFFRACTION97
2.3287-2.3710.22055600.169710109X-RAY DIFFRACTION97
2.371-2.41660.21235350.165910210X-RAY DIFFRACTION97
2.4166-2.46580.22735450.17310301X-RAY DIFFRACTION97
2.4658-2.51940.2175290.171410110X-RAY DIFFRACTION97
2.5194-2.5780.22245000.167810175X-RAY DIFFRACTION97
2.578-2.64240.20625350.170310333X-RAY DIFFRACTION98
2.6424-2.71370.22145560.171610283X-RAY DIFFRACTION98
2.7137-2.79350.21035480.168210138X-RAY DIFFRACTION98
2.7935-2.88350.20395640.1710224X-RAY DIFFRACTION98
2.8835-2.98640.20665320.174710227X-RAY DIFFRACTION98
2.9864-3.10580.21445380.173810272X-RAY DIFFRACTION98
3.1058-3.24680.19425630.168810270X-RAY DIFFRACTION98
3.2468-3.41760.18655550.16710324X-RAY DIFFRACTION98
3.4176-3.63110.18565340.159810199X-RAY DIFFRACTION98
3.6311-3.91050.18045570.157910337X-RAY DIFFRACTION98
3.9105-4.30220.1865650.15710262X-RAY DIFFRACTION98
4.3022-4.92060.1685820.147110365X-RAY DIFFRACTION98
4.9206-6.18390.19545400.166910256X-RAY DIFFRACTION99
6.1839-24.96270.20655690.182410327X-RAY DIFFRACTION99
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)
10.49670.20660.01320.35790.0180.1602-0.01920.0310.0502-0.03610.0118-0.0355-0.06520.01220.02060.0995-0.01510.00750.01920.00320.075718.48988.552174.8291
20.1144-0.03820.0280.2557-0.05810.1070.0028-0.01240.00490.0252-0.0042-0.02550.0155-0.0054-0.00330.07150.0073-0.0059-0.0028-0.00510.042511.934-14.10690.3876
30.1592-0.05570.01410.1914-0.0050.14250.01170.0173-0.0289-0.0164-0.00370.05120.0583-0.0238-0.00820.098-0.00320.00340.0209-0.00880.0752-0.2297-34.907177.7313
40.3830.0793-0.03360.7367-0.0290.358-0.0090.03090.0357-0.04820.0007-0.0264-0.01330.03080.00510.13180.01250.0060.0621-0.00650.0615.387-29.646865.486
50.43010.0133-0.2320.33790.00370.4870.02520.00520.00470.00140.0048-0.10090.03630.1267-0.01260.14680.0808-0.00380.0966-0.03180.087129.4332-57.8624.0638
60.118-0.0925-0.02340.17680.02730.1120.02770.04170.0057-0.0772-0.04260.00480.0016-0.0186-0.01520.1820.0813-0.03690.0462-0.03680.06573.9467-47.467517.3381
70.1444-0.03980.06660.1826-0.03420.23710.02450.0019-0.0356-0.0139-0.03840.0881-0.0145-0.1068-0.00810.11810.0448-0.0150.0754-0.04130.085-10.9808-37.122937.6787
80.6616-0.1696-0.03160.50950.05170.357-0.0379-0.00340.00250.0014-0.0006-0.0539-0.01370.04990.00680.1490.0215-0.01690.0703-0.00740.05917.7568-28.93640.1169
90.3491-0.0731-0.11820.54450.28090.48680.0004-0.01130.1156-0.00290.01980.0509-0.0798-0.05980.00370.04280.01810.02030.15350.01010.09499.1872-38.893194.3623
100.2069-0.0422-0.03080.07110.00560.0846-0.0116-0.0937-0.00730.01460.0153-0.00230.0195-0.003-0.00870.0291-0.0060.00950.20410.02470.058428.1879-59.0733200.1803
110.1965-0.01360.07090.1521-0.05370.21420.0015-0.0314-0.0528-0.04060.0046-0.03010.06050.0292-0.00930.0457-0.00230.01660.13710.02320.072743.2485-68.3352179.4444
120.6798-0.1883-0.07790.55420.02540.37720.01180.02330.0642-0.0001-0.001-0.0031-0.0598-0.0021-0.0020.0712-0.00830.01480.16330.02950.064144.0364-47.8589177.9089
130.27150.1076-0.03840.70660.04790.19450.0006-0.06910.06620.0694-0.0137-0.0664-0.06670.09830.02150.0686-0.0489-0.00220.1286-0.01550.1049-3.2133-22.8048144.6567
140.30210.03050.04120.1263-0.02040.1005-0.01370.0020.0434-0.01570.007-0.00490.00730.0024-0.00330.0048-0.03030.01220.07680.02260.048-22.1614-35.9179128.2822
150.24-0.03890.07080.1316-0.04280.24420.0047-0.012-0.0589-0.01210.02090.02580.065-0.0073-0.00620.0508-0.02710.00070.07970.01950.0801-37.1874-55.4867139.8493
160.65520.18680.00960.47880.03160.34880.0196-0.05140.04320.0203-0.0107-0.0349-0.03620.01250.00110.062-0.01260.00660.11820.01350.0685-37.9715-39.7449152.957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 61:220)
2X-RAY DIFFRACTION2(chain A and resid 221:598)
3X-RAY DIFFRACTION3(chain A and resid 599:881)
4X-RAY DIFFRACTION4(chain A and resid 882:963)
5X-RAY DIFFRACTION5(chain B and resid 61:220)
6X-RAY DIFFRACTION6(chain B and resid 221:598)
7X-RAY DIFFRACTION7(chain B and resid 599:881)
8X-RAY DIFFRACTION8(chain B and resid 882:963)
9X-RAY DIFFRACTION9(chain C and resid 61:220)
10X-RAY DIFFRACTION10(chain C and resid 221:598)
11X-RAY DIFFRACTION11(chain C and resid 599:881)
12X-RAY DIFFRACTION12(chain C and resid 882:963)
13X-RAY DIFFRACTION13(chain D and resid 61:220)
14X-RAY DIFFRACTION14(chain D and resid 221:598)
15X-RAY DIFFRACTION15(chain D and resid 599:881)
16X-RAY DIFFRACTION16(chain D and resid 882:963)

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  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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