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- PDB-1w2d: Human Inositol (1,4,5)-trisphosphate 3-kinase complexed with Mn2+... -

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Basic information

Entry
Database: PDB / ID: 1w2d
TitleHuman Inositol (1,4,5)-trisphosphate 3-kinase complexed with Mn2+/ADP/Ins(1,3,4,5)P4
ComponentsINOSITOL-TRISPHOSPHATE 3-KINASE A
KeywordsTRANSFERASE / INOSITOL PHOSPHATE KINASE / ADP / IP4
Function / homology
Function and homology information


inositol-trisphosphate 3-kinase / inositol tetrakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / inositol phosphate biosynthetic process / modification of postsynaptic actin cytoskeleton / inositol metabolic process / postsynaptic actin cytoskeleton / positive regulation of dendritic spine morphogenesis / calcium/calmodulin-dependent protein kinase activity / dendritic spine maintenance ...inositol-trisphosphate 3-kinase / inositol tetrakisphosphate kinase activity / inositol-1,4,5-trisphosphate 3-kinase activity / inositol phosphate biosynthetic process / modification of postsynaptic actin cytoskeleton / inositol metabolic process / postsynaptic actin cytoskeleton / positive regulation of dendritic spine morphogenesis / calcium/calmodulin-dependent protein kinase activity / dendritic spine maintenance / Synthesis of IP3 and IP4 in the cytosol / phosphatidylinositol phosphate biosynthetic process / cellular response to calcium ion / regulation of synaptic plasticity / small GTPase binding / response to calcium ion / actin cytoskeleton organization / dendritic spine / cytoskeleton / calmodulin binding / glutamatergic synapse / signal transduction / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Inositol polyphosphate kinase / Inositol polyphosphate kinase / Inositol polyphosphate kinase superfamily / Inositol polyphosphate kinase / D-amino Acid Aminotransferase; Chain A, domain 1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE / ADENOSINE-5'-DIPHOSPHATE / : / Inositol-trisphosphate 3-kinase A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.94 Å
AuthorsGonzalez, B. / Schell, M.J. / Irvine, R.F. / Williams, R.L.
CitationJournal: Mol.Cell / Year: 2004
Title: Structure of a Human Inositol 1,4,5-Trisphosphate 3-Kinase; Substrate Binding Reveals Why It is not a Phosphoinositide 3-Kinase
Authors: Gonzalez, B. / Schell, M.J. / Letcher, A.J. / Veprintsev, D.B. / Irvine, R.F. / Williams, R.L.
History
DepositionJul 1, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 9, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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 / _struct_conn.pdbx_dist_value / _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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INOSITOL-TRISPHOSPHATE 3-KINASE A
B: INOSITOL-TRISPHOSPHATE 3-KINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,10411
Polymers60,8512
Non-polymers2,2539
Water4,666259
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A: INOSITOL-TRISPHOSPHATE 3-KINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6006
Polymers30,4261
Non-polymers1,1745
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: INOSITOL-TRISPHOSPHATE 3-KINASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5045
Polymers30,4261
Non-polymers1,0784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.054, 97.411, 190.844
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-2059-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.21043, 0.59706, 0.77411), (0.58557, -0.55709, 0.58886), (0.78283, 0.57721, -0.23239)
Vector: -61.594, 8.6267, 56.443)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein INOSITOL-TRISPHOSPHATE 3-KINASE A / INOSITOL 1 / 4 / 5-TRISPHOSPHATE 3-KINASE / IP3-3K


Mass: 30425.650 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN, RESIDUES 197-461
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P23677, EC: 2.1.7.127

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Non-polymers , 5 types, 268 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-4IP / INOSITOL-(1,3,4,5)-TETRAKISPHOSPHATE


Mass: 500.075 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H16O18P4
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.6 Å3/Da / Density % sol: 47.7 %
Crystal growpH: 8 / Details: 0.82 M NA CITRATE, 0.1 M NACL, 0.1 M TRIS PH 8.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 2003 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.94→49.51 Å / Num. obs: 48642 / % possible obs: 97.2 % / Observed criterion σ(I): 2 / Redundancy: 6.83 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 8.5537
Reflection shellResolution: 1.94→2.04 Å / Redundancy: 6.32 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.6 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.94→48.8 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.904 / SU B: 4.26 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.267 2453 5.1 %RANDOM
Rwork0.226 ---
obs0.228 46068 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.05 Å20 Å20 Å2
2---0.08 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.94→48.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4138 0 127 259 4524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214339
X-RAY DIFFRACTIONr_bond_other_d0.0150.023919
X-RAY DIFFRACTIONr_angle_refined_deg1.7512.0025865
X-RAY DIFFRACTIONr_angle_other_deg0.98139090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9465511
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1130.2630
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024698
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02919
X-RAY DIFFRACTIONr_nbd_refined0.220.2958
X-RAY DIFFRACTIONr_nbd_other0.2610.24599
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.22444
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2262
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.219
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0881.52547
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.86624083
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.64531792
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9994.51782
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.372 179
Rwork0.284 3383

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