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- PDB-3hii: Crystal structure of human diamine oxidase in complex with the in... -

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Basic information

Entry
Database: PDB / ID: 3hii
TitleCrystal structure of human diamine oxidase in complex with the inhibitor pentamidine
ComponentsAmiloride-sensitive amine oxidase
KeywordsOXIDOREDUCTASE / copper amine oxidase / topaquinone / TPQ / diamine oxidase / DAO / human / pentamidine / Glycoprotein / Heparin-binding / Metal-binding / Secreted
Function / homology
Function and homology information


diamine oxidase / putrescine metabolic process / histamine oxidase activity / putrescine oxidase activity / diamine oxidase activity / primary methylamine oxidase activity / Phase I - Functionalization of compounds / bicellular tight junction / quinone binding / specific granule lumen ...diamine oxidase / putrescine metabolic process / histamine oxidase activity / putrescine oxidase activity / diamine oxidase activity / primary methylamine oxidase activity / Phase I - Functionalization of compounds / bicellular tight junction / quinone binding / specific granule lumen / peroxisome / heparin binding / copper ion binding / calcium ion binding / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / : / Copper amine oxidase copper-binding site signature. / : / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 ...Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / : / Copper amine oxidase copper-binding site signature. / : / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain / Beta-galactosidase; Chain A, domain 5 / Nuclear Transport Factor 2; Chain: A, / Distorted Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / 1,5-BIS(4-AMIDINOPHENOXY)PENTANE / Diamine oxidase [copper-containing]
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / BY REFINEMENT / Resolution: 2.149 Å
AuthorsMcGrath, A.P. / Guss, J.M.
CitationJournal: Biochemistry / Year: 2009
Title: Structure and inhibition of human diamine oxidase
Authors: McGrath, A.P. / Hilmer, K.M. / Collyer, C.A. / Shepard, E.M. / Elmore, B.O. / Brown, D.E. / Dooley, D.M. / Guss, J.M.
History
DepositionMay 20, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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 / 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.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
Revision 2.1Nov 10, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Nov 1, 2023Group: 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: Amiloride-sensitive amine oxidase
B: Amiloride-sensitive amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,69617
Polymers166,9282
Non-polymers3,76915
Water16,502916
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22780 Å2
ΔGint-92 kcal/mol
Surface area46890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.455, 94.690, 196.279
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Amiloride-sensitive amine oxidase / Diamine oxidase / DAO / Amiloride-binding protein / ABP / Histaminase / Kidney amine oxidase / KAO


Mass: 83463.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ABP1 / Cell line (production host): Schneider 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P19801, diamine oxidase

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Sugars , 2 types, 6 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.: 1
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

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Non-polymers , 5 types, 925 molecules

#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PNT / 1,5-BIS(4-AMIDINOPHENOXY)PENTANE


Mass: 340.419 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H24N4O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 916 / 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: 2.58 Å3/Da / Density % sol: 52.24 % / Mosaicity: 0.431 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M bis-tris propane, 20%(w/v) PEG 3350, 0.2M sodium sulfate, pH 7.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 5, 2008 / Details: OSMIC MIRRORS
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.149→50 Å / Num. all: 89751 / Num. obs: 89751 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 29.96 Å2 / Rmerge(I) obs: 0.103 / Χ2: 1.067 / Net I/σ(I): 9.903
Reflection shellResolution: 2.149→2.23 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 2.7 / Num. unique all: 8090 / Χ2: 1.041 / % possible all: 87.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.5.0063phasing
RefinementMethod to determine structure: BY REFINEMENT
Starting model: PDB ENTRY 3HI7

3hi7


Resolution: 2.149→25.84 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.926 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.866 / SU B: 4.494 / SU ML: 0.118 / SU R Cruickshank DPI: 0.245 / SU Rfree: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22093 4554 5.1 %RANDOM
Rwork0.18159 ---
obs0.18359 85093 94.98 %-
all-85093 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.23 Å2 / Biso mean: 21.017 Å2 / Biso min: 11.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.2 Å20 Å20 Å2
2---0.94 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.149→25.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11354 0 241 916 12511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02112215
X-RAY DIFFRACTIONr_bond_other_d0.0010.028166
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.95716761
X-RAY DIFFRACTIONr_angle_other_deg0.784319717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52151482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.922.92572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.793151721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9851576
X-RAY DIFFRACTIONr_chiral_restr0.070.21780
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113734
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022697
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4311.57254
X-RAY DIFFRACTIONr_mcbond_other0.0811.52876
X-RAY DIFFRACTIONr_mcangle_it0.808211775
X-RAY DIFFRACTIONr_scbond_it1.19134961
X-RAY DIFFRACTIONr_scangle_it1.9324.54963
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.149→2.204 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 290 -
Rwork0.232 5522 -
all-5812 -
obs--84.91 %

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