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- PDB-4nzn: Crystal structure of the catalytic domain of PPIP5K2 in complex w... -

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Basic information

Entry
Database: PDB / ID: 4nzn
TitleCrystal structure of the catalytic domain of PPIP5K2 in complex with AMPPNP and 2-O-BN-5-PA-INSP4
ComponentsInositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / ATP-grasp Fold / Inositol Pyrophosphate Kinase / drug discovery / kinase / enzymology / inositol pyrophosphates / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


diphosphoinositol-pentakisphosphate 1-kinase / diphosphoinositol pentakisphosphate kinase activity / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol hexakisphosphate 5-kinase activity / inositol hexakisphosphate kinase activity / Synthesis of pyrophosphates in the cytosol / inositol phosphate metabolic process ...diphosphoinositol-pentakisphosphate 1-kinase / diphosphoinositol pentakisphosphate kinase activity / 5-diphosphoinositol pentakisphosphate 1-kinase activity / inositol hexakisphosphate 1-kinase activity / inositol hexakisphosphate 3-kinase activity / inositol-1,3,4,5,6-pentakisphosphate kinase activity / inositol hexakisphosphate 5-kinase activity / inositol hexakisphosphate kinase activity / Synthesis of pyrophosphates in the cytosol / inositol phosphate metabolic process / inositol phosphate biosynthetic process / inositol metabolic process / sensory perception of sound / ATP binding / cytosol
Similarity search - Function
Rossmann fold - #11950 / Histidine acid phosphatase, VIP1 family / VIP1, N-terminal / Diphosphoinositol pentakisphosphate kinase 2 N-terminal domain / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / ATP-grasp fold, B domain ...Rossmann fold - #11950 / Histidine acid phosphatase, VIP1 family / VIP1, N-terminal / Diphosphoinositol pentakisphosphate kinase 2 N-terminal domain / Histidine acid phosphatases phosphohistidine signature. / Histidine acid phosphatase active site / Histidine phosphatase superfamily, clade-2 / Histidine phosphatase superfamily (branch 2) / Histidine phosphatase superfamily / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2OU / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsWang, H. / Shears, S.B.
CitationJournal: Chem.Biol. / Year: 2014
Title: Synthetic Inositol Phosphate Analogs Reveal that PPIP5K2 Has a Surface-Mounted Substrate Capture Site that Is a Target for Drug Discovery.
Authors: Wang, H. / Godage, H.Y. / Riley, A.M. / Weaver, J.D. / Shears, S.B. / Potter, B.V.
History
DepositionDec 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8606
Polymers37,5691
Non-polymers1,2915
Water7,026390
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.316, 110.690, 41.301
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 2 / Diphosphoinositol pentakisphosphate kinase 2 / Histidine acid phosphatase domain-containing protein ...Diphosphoinositol pentakisphosphate kinase 2 / Histidine acid phosphatase domain-containing protein 1 / InsP6 and PP-IP5 kinase 2 / VIP1 homolog 2 / hsVIP2


Mass: 37568.891 Da / Num. of mol.: 1 / Fragment: ATP-grasp Kinase domain, UNP residues 41-366
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIP5K2, HISPPD1, KIAA0433, VIP2 / Plasmid: pDest566 / Production host: Escherichia coli (E. coli) / Strain (production host): Arctic Express (DE3)
References: UniProt: O43314, inositol-hexakisphosphate 5-kinase, diphosphoinositol-pentakisphosphate 1-kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-2OU / (2-{[(1s,2R,3R,4r,5S,6S)-4-(benzyloxy)-2,3,5,6-tetrakis(phosphonooxy)cyclohexyl]oxy}-2-oxoethyl)phosphonic acid


Mass: 712.215 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25O22P5
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.72 Å3/Da / Density % sol: 54.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMPPNP with 2 mM CdCl2. Soaking under 22% PEG3350, 10 mM MgCl2 0.1 M Sodium Acetate, pH5.2 with 5 mM 2-O-Bn-5-PA-InsP4, 3 days, ...Details: 12% (w/v) PEG 3350, 20 mM MgCl2, 0.1 M HEPES, pH 7.0, 1 mM AMPPNP with 2 mM CdCl2. Soaking under 22% PEG3350, 10 mM MgCl2 0.1 M Sodium Acetate, pH5.2 with 5 mM 2-O-Bn-5-PA-InsP4, 3 days, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 27, 2013
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 42399 / Num. obs: 42399 / % possible obs: 99.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rsym value: 0.071 / Net I/σ(I): 28
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 2.5 / Num. unique all: 2037 / Rsym value: 0.531 / % possible all: 97.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3T9B

3t9b


Resolution: 1.75→33.12 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.7 / SU ML: 0.054 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17969 2619 6.2 %RANDOM
Rwork0.14096 ---
all0.14334 39720 --
obs0.14334 39720 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.359 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.75→33.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 76 390 3070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.022780
X-RAY DIFFRACTIONr_bond_other_d0.0010.022609
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9973786
X-RAY DIFFRACTIONr_angle_other_deg0.7953.0036031
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3285334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44724.094127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71615478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0211518
X-RAY DIFFRACTIONr_chiral_restr0.1010.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02626
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_it2.0152.0611321
X-RAY DIFFRACTIONr_mcbond_other1.9192.0561320
X-RAY DIFFRACTIONr_mcangle_it2.513.0891657
X-RAY DIFFRACTIONr_mcangle_other2.5093.0931658
X-RAY DIFFRACTIONr_scbond_it2.6482.5231459
X-RAY DIFFRACTIONr_scbond_other2.6472.5261460
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4673.6542129
X-RAY DIFFRACTIONr_long_range_B_refined5.42719.2773464
X-RAY DIFFRACTIONr_long_range_B_other4.25418.263256
X-RAY DIFFRACTIONr_rigid_bond_restr2.46435389
X-RAY DIFFRACTIONr_sphericity_free36.6795116
X-RAY DIFFRACTIONr_sphericity_bonded10.13255598
LS refinement shellResolution: 1.75→1.789 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 188 -
Rwork0.227 2660 -
obs--91.02 %

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