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- PDB-2pnc: Crystal Structure of Bovine Plasma Copper-Containing Amine Oxidas... -

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Basic information

Entry
Database: PDB / ID: 2pnc
TitleCrystal Structure of Bovine Plasma Copper-Containing Amine Oxidase in Complex with Clonidine
ComponentsCopper amine oxidase, liver isozyme
KeywordsOXIDOREDUCTASE / AMINE OXIDASE / QUINOENZYME / TPQ / clonidine
Function / homology
Function and homology information


Phase I - Functionalization of compounds / primary-amine oxidase / primary methylamine oxidase activity / amine metabolic process / quinone binding / early endosome / copper ion binding / endoplasmic reticulum / Golgi apparatus / 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
triacetyl-beta-chitotriose / 2,6-DICHLORO-N-IMIDAZOLIDIN-2-YLIDENEANILINE / COPPER (II) ION / Primary amine oxidase, liver isozyme
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCendron, L. / Holt, A. / Smith, D.J. / Zanotti, G. / Rigo, A. / Di Paolo, M.L.
Citation
Journal: Mol.Pharmacol. / Year: 2008
Title: Multiple binding sites for substrates and modulators of semicarbazide-sensitive amine oxidases: kinetic consequences
Authors: Holt, A. / Smith, D.J. / Cendron, L. / Zanotti, G. / Rigo, A. / Di Paolo, M.L.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: Crystal structure of amine oxidase from bovine serum.
Authors: Lunelli, M. / Di Paolo, M.L. / Biadene, M. / Calderone, V. / Battistutta, R. / Scarpa, M. / Rigo, A. / Zanotti, G.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and Preliminary X-Ray Data of Amine Oxidase from Bovine Serum
Authors: Calderone, V. / Di Paolo, M.L. / Trabucco, M. / Biadene, M. / Battistutta, R. / Rigo, A. / Zanotti, G.
#3: Journal: Structure / Year: 1995
Title: Crystal Structure of a Quinoenzyme: Copper Amine Oxidase of Escherichia Coli at 2 A Resolution
Authors: Parsons, M.R. / Convery, M.A. / Wilmot, C.M. / Yadav, K.D. / Blakeley, V. / Corner, A.S. / Phillips, S.E. / McPherson, M.J. / Knowles, P.F.
#4: Journal: Structure / Year: 1996
Title: Crystal Structure of a Eukaryotic (Pea Seedling) Copper-Containing Amine Oxidase at 2.2 A Resolution
Authors: Kumar, V. / Dooley, D.M. / Freeman, H.C. / Guss, J.M. / Harvey, I. / Mcguirl, M.A. / Wilce, M.C. / Zubak, V.M.
#5: Journal: Biochemistry / Year: 2003
Title: The Crystal Structure of Pichia Pastoris Lysyl Oxidase
Authors: Duff, A.P. / Cohen, A.E. / Ellis, P.J. / Kuchar, J.A. / Langley, D.B. / Shepard, E.M. / Dooley, D.M. / Freeman, H.C. / Guss, J.M.
History
DepositionApr 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Jul 25, 2012Group: Other
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 / entity_name_com / 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_molecule_features / 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.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_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_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 / _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 2.1Aug 30, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper amine oxidase, liver isozyme
B: Copper amine oxidase, liver isozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,01315
Polymers165,9042
Non-polymers2,10913
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13450 Å2
ΔGint-167 kcal/mol
Surface area42290 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.360, 131.956, 134.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLNGLNAA57 - 7741 - 61
21GLNGLNGLNGLNBB57 - 7741 - 61
32VALVALLEULEUAA83 - 19467 - 178
42VALVALLEULEUBB83 - 19467 - 178
53VALVALVALVALAA260 - 285244 - 269
63VALVALVALVALBB260 - 285244 - 269
74ASPASPPROPROAA475 - 547459 - 531
84ASPASPPROPROBB475 - 547459 - 531
95ALAALAGLUGLUAA549 - 638533 - 622
105ALAALAGLUGLUBB549 - 638533 - 622
116GLUGLUGLYGLYAA640 - 680624 - 664
126GLUGLUGLYGLYBB640 - 680624 - 664
137ARGARGARGARGAA321 - 440305 - 424
147ARGARGARGARGBB321 - 440305 - 424
DetailsThe biological assembly is the dimer present in the asymetric unit

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Copper amine oxidase, liver isozyme / Amine oxidase [copper-containing] / Serum amine oxidase / SAO


Mass: 82951.805 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Tissue: PLASMA / References: UniProt: Q29437, EC: 1.4.3.6
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE

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Non-polymers , 5 types, 342 molecules

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


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


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-CLU / 2,6-DICHLORO-N-IMIDAZOLIDIN-2-YLIDENEANILINE / CLONIDINE


Mass: 230.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H9Cl2N3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.09 Å3/Da / Density % sol: 41.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.4
Details: KH2PO4 (0.2 M, pH 7.4) and PEG 3350 (20%, w/v), VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97984 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97984 Å / Relative weight: 1
ReflectionResolution: 2.4→34 Å / Num. all: 47787 / Num. obs: 47787 / % possible obs: 86.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 3.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 1.5 / Num. unique all: 6507 / % possible all: 82.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1TU5

1tu5


Resolution: 2.4→29.11 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.896 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.978 / ESU R Free: 0.309 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25227 2429 5.1 %RANDOM
Rwork0.23695 ---
all0.2389 47787 --
obs0.23774 45208 86.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.622 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2---0.31 Å20 Å2
3----0.07 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9852 0 121 331 10304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.02210271
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8771.95813996
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.66151236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.80323.548496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.722151514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8231568
X-RAY DIFFRACTIONr_chiral_restr0.0630.21482
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.028071
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.35141
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3340.56816
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2040.5774
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.130.54
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1770.356
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.510
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.85926208
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.89339998
X-RAY DIFFRACTIONr_scbond_it4.66224063
X-RAY DIFFRACTIONr_scangle_it6.48633998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1928medium positional0.180.5
1882loose positional0.45
1928medium thermal3.232
1882loose thermal4.5910
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 177 -
Rwork0.325 3093 -
obs--82 %

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