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- PDB-4p8q: Crystal Structure of Human Insulin Regulated Aminopeptidase with ... -

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Basic information

Entry
Database: PDB / ID: 4p8q
TitleCrystal Structure of Human Insulin Regulated Aminopeptidase with Alanine in Active Site
ComponentsLeucyl-cystinyl aminopeptidaseLeucyl/cystinyl aminopeptidase
KeywordsHYDROLASE / Aminopeptidase / Metallopeptidase
Function / homology
Function and homology information


cystinyl aminopeptidase / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / negative regulation of cold-induced thermogenesis / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / early endosome lumen / female pregnancy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Endosomal/Vacuolar pathway ...cystinyl aminopeptidase / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent / negative regulation of cold-induced thermogenesis / peptide catabolic process / metalloaminopeptidase activity / aminopeptidase activity / early endosome lumen / female pregnancy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Endosomal/Vacuolar pathway / peptide binding / protein catabolic process / cytoplasmic vesicle membrane / regulation of blood pressure / protein polyubiquitination / metallopeptidase activity / Antigen processing: Ubiquitination & Proteasome degradation / cell-cell signaling / lysosomal membrane / perinuclear region of cytoplasm / signal transduction / proteolysis / zinc ion binding / extracellular region / membrane / plasma membrane / cytosol / 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
Unknown ligand / Leucyl-cystinyl aminopeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.02 Å
AuthorsHermans, S.J. / Ascher, D.B. / Hancock, N.C. / Holien, J.K. / Michell, B. / Morton, C.J. / Parker, M.W.
CitationJournal: Protein Sci. / Year: 2015
Title: Crystal structure of human insulin-regulated aminopeptidase with specificity for cyclic peptides.
Authors: Hermans, S.J. / Ascher, D.B. / Hancock, N.C. / Holien, J.K. / Michell, B.J. / Yeen Chai, S. / Morton, C.J. / Parker, M.W.
History
DepositionMar 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / diffrn_source / entity / entity_src_gen / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / refine_hist / 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.occupancy / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _struct_asym.entity_id / _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
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Leucyl-cystinyl aminopeptidase
B: Leucyl-cystinyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,14022
Polymers200,4542
Non-polymers4,68620
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7530 Å2
ΔGint-22 kcal/mol
Surface area68810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.323, 256.051, 71.132
Angle α, β, γ (deg.)90.00, 115.12, 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 Leucyl-cystinyl aminopeptidase / Leucyl/cystinyl aminopeptidase / Cystinyl aminopeptidase / Insulin-regulated membrane aminopeptidase / Insulin-responsive ...Cystinyl aminopeptidase / Insulin-regulated membrane aminopeptidase / Insulin-responsive aminopeptidase / IRAP / Oxytocinase / OTase / Placental leucine aminopeptidase / P-LAP


Mass: 100226.984 Da / Num. of mol.: 2 / Fragment: UNP residues 155-1025
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LNPEP, OTASE / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9UIQ6, cystinyl aminopeptidase

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Sugars , 2 types, 16 molecules

#2: 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: obtained synthetically
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: 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.: 11 / 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 , 3 types, 59 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.81 Å3/Da / Density % sol: 56.3 % / Description: Rod
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG 3000, tris hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 3.02→48.42 Å / Num. obs: 42874 / % possible obs: 99.5 % / Redundancy: 3.8 % / Biso Wilson estimate: 85.07 Å2 / Rmerge(I) obs: 0.111 / Net I/σ(I): 11.2
Reflection shellResolution: 3.02→3.19 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.692 / Mean I/σ(I) obs: 1.9 / % possible all: 97.7

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Processing

SoftwareName: BUSTER / Version: 2.10.0 / Classification: refinement
RefinementResolution: 3.02→48.42 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.879 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.414
RfactorNum. reflection% reflectionSelection details
Rfree0.25 2157 5.04 %RANDOM
Rwork0.19 ---
obs0.193 42833 99.1 %-
Displacement parametersBiso mean: 68.35 Å2
Baniso -1Baniso -2Baniso -3
1--6.9855 Å20 Å28.5708 Å2
2--0.695 Å20 Å2
3---6.2906 Å2
Refine analyzeLuzzati coordinate error obs: 0.508 Å
Refinement stepCycle: final / Resolution: 3.02→48.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13779 0 306 55 14140
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00914470HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1519677HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5028SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes359HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2062HARMONIC5
X-RAY DIFFRACTIONt_it14470HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.52
X-RAY DIFFRACTIONt_other_torsion20.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1949SEMIHARMONIC5
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_contact16737SEMIHARMONIC4
LS refinement shellResolution: 3.02→3.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3119 168 5.69 %
Rwork0.2231 2785 -
all0.2281 2953 -
obs--99.12 %

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