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- PDB-4btw: Crystal structure of human vascular adhesion protein-1 in complex... -

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Basic information

Entry
Database: PDB / ID: 4btw
TitleCrystal structure of human vascular adhesion protein-1 in complex with pyridazinone inhibitors
ComponentsMEMBRANE PRIMARY AMINE OXIDASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds / microvillus / quinone binding / early endosome / cell adhesion / inflammatory response ...primary-amine oxidase / aliphatic amine oxidase activity / primary methylamine oxidase activity / amine metabolic process / Phase I - Functionalization of compounds / microvillus / quinone binding / early endosome / cell adhesion / inflammatory response / protein heterodimerization activity / copper ion binding / response to antibiotic / calcium ion binding / Golgi apparatus / cell surface / endoplasmic reticulum / identical protein binding / membrane / plasma membrane / cytoplasm
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 / Chem-JW7 / Amine oxidase [copper-containing] 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBligt-Linden, E. / Pihlavisto, M. / Szatmari, I. / Otwinowski, Z. / Smith, D.J. / Lazar, L. / Fulop, F. / Salminen, T.A.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Novel Pyridazinone Inhibitors for Vascular Adhesion Protein- 1 (Vap-1): Old Target - New Inhibition Mode.
Authors: Bligt-Linden, E. / Pihlavisto, M. / Szatmari, I. / Otwinowski, Z. / Smith, D.J. / Lazar, L. / Fulop, F. / Salminen, T.A.
History
DepositionJun 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / 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_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_database_status.status_code_sf / _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_label_asym_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 / _pdbx_unobs_or_zero_occ_atoms.label_asym_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: MEMBRANE PRIMARY AMINE OXIDASE
B: MEMBRANE PRIMARY AMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,42720
Polymers163,7942
Non-polymers4,63418
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21070 Å2
ΔGint-94.6 kcal/mol
Surface area47380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)226.473, 226.473, 219.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein MEMBRANE PRIMARY AMINE OXIDASE / COPPER AMINE OXIDASE / HPAO / SEMICARBAZIDE-SENSITIVE AMINE OXIDASE / SSAO / VASCULAR ADHESION ...COPPER AMINE OXIDASE / HPAO / SEMICARBAZIDE-SENSITIVE AMINE OXIDASE / SSAO / VASCULAR ADHESION PROTEIN 1 / VAP-1


Mass: 81896.852 Da / Num. of mol.: 2 / Fragment: RESIDUES 27-763 / Source method: isolated from a natural source
Details: TYR471 POST TRANSLATIONALLY MODIFIED TO TOPAQUINONE
Source: (natural) HOMO SAPIENS (human) / Tissue: SERUM / References: UniProt: Q16853, primary-amine oxidase

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Sugars , 4 types, 10 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.: 2
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)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[beta-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[DManpb1-6]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]/1-1-2-3-2/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)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#7: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
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 , 4 types, 114 molecules

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


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-JW7 / 5-(cyclohexylamino)-2-phenyl-6-(1H-1,2,4-triazol-5-yl)-3(2H)-pyridazinone


Mass: 336.391 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H20N6O
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 5.01 Å3/Da / Density % sol: 75.26 % / Description: NONE
Crystal growDetails: 0.6-0.75 M NA/K TARTRATE, 0.2 M NACL, 0.1 M HEPES PH 7.4-7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.00005
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 60329 / % possible obs: 96 % / Observed criterion σ(I): 1.46 / Redundancy: 9.2 % / Rmerge(I) obs: 0.32 / Net I/σ(I): 3.5
Reflection shellResolution: 2.8→2.82 Å / Redundancy: 5.7 % / % possible all: 82.6

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Processing

Software
NameVersionClassification
HKLdata reduction
HKLdata scaling
CCP4phasing
MOLREPphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1US1

1us1


Resolution: 2.8→49.39 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.88 / SU B: 13.413 / SU ML: 0.248 / Cross valid method: THROUGHOUT / ESU R: 0.576 / ESU R Free: 0.353 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26032 3176 5 %RANDOM
Rwork0.20504 ---
obs0.20781 60329 77.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.8→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11171 0 296 106 11573
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01911878
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210732
X-RAY DIFFRACTIONr_angle_refined_deg1.951.97116184
X-RAY DIFFRACTIONr_angle_other_deg0.8923.00124563
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.33751414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21723.059559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.319151669
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.431580
X-RAY DIFFRACTIONr_chiral_restr0.0920.21725
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113482
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022944
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_it4.5495.9885669
X-RAY DIFFRACTIONr_mcbond_other4.5485.9875668
X-RAY DIFFRACTIONr_mcangle_it7.1338.9667074
X-RAY DIFFRACTIONr_mcangle_other7.1348.9677075
X-RAY DIFFRACTIONr_scbond_it4.3366.4386208
X-RAY DIFFRACTIONr_scbond_other4.3366.4386209
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.8749.5419111
X-RAY DIFFRACTIONr_long_range_B_refined10.42650.09413933
X-RAY DIFFRACTIONr_long_range_B_other10.42550.09513930
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 106 -
Rwork0.314 1648 -
obs--29.65 %

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