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Basic information

Entry
Database: PDB / ID: 4m5k
TitleThe Identification, Analysis and Structure-Based Development of Novel Inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase
Components2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / FOLATE BIOSYNTHESIS / Diphosphotransferases / PTERIN / ATP binding / Inhibitor / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase activity / folic acid biosynthetic process / tetrahydrofolate biosynthetic process / kinase activity / phosphorylation / magnesium ion binding / ATP binding
Similarity search - Function
7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase signature. / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase, HPPK / 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK superfamily / 7,8-dihydro-6-hydroxymethylpterin-pyrophosphokinase (HPPK) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / Chem-YH3 / 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.296 Å
AuthorsYun, M. / Hoagland, D. / Kumar, G. / Waddell, B. / Rock, C.O. / Lee, R.E. / White, S.W.
CitationJournal: Bioorg.Med.Chem. / Year: 2014
Title: The identification, analysis and structure-based development of novel inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase.
Authors: Yun, M.K. / Hoagland, D. / Kumar, G. / Waddell, M.B. / Rock, C.O. / Lee, R.E. / White, S.W.
History
DepositionAug 8, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 16, 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: 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4137
Polymers18,3801
Non-polymers1,0336
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.955, 57.917, 38.467
Angle α, β, γ (deg.)90.00, 115.41, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase / 6-hydroxymethyl-7 / 8-dihydropterin pyrophosphokinase / PPPK / 7 / 8-dihydro-6-hydroxymethylpterin- ...6-hydroxymethyl-7 / 8-dihydropterin pyrophosphokinase / PPPK / 7 / 8-dihydro-6-hydroxymethylpterin-pyrophosphokinase / HPPK


Mass: 18380.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: folK, b0142, JW0138 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P26281, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase

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Non-polymers , 5 types, 200 molecules

#2: Chemical ChemComp-APC / DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER / ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-CPP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-YH3 / 2-amino-8-{[2-(3-methylphenyl)-2-oxoethyl]sulfanyl}-1,9-dihydro-6H-purin-6-one


Mass: 315.350 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H13N5O2S
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 1.97 Å3/Da / Density % sol: 37.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.2M calcium chloride, 25% PEG 4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 17, 2013 / Details: Rosenbaum-Rock double-crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.296→50 Å / Num. obs: 34707 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rsym value: 0.064 / Net I/σ(I): 25.4
Reflection shellResolution: 1.296→1.33 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 1969 / Rsym value: 0.236 / % possible all: 77.2

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4M5G

4m5g


Resolution: 1.296→34.746 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1743 1725 4.97 %Random
Rwork0.1491 ---
obs0.1504 34683 98 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.801 Å2 / ksol: 0.396 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.9381 Å20 Å21.3883 Å2
2---0.4448 Å2-0 Å2
3----0.4932 Å2
Refinement stepCycle: LAST / Resolution: 1.296→34.746 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1275 0 62 194 1531
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011395
X-RAY DIFFRACTIONf_angle_d1.3061928
X-RAY DIFFRACTIONf_dihedral_angle_d16.886523
X-RAY DIFFRACTIONf_chiral_restr0.075204
X-RAY DIFFRACTIONf_plane_restr0.005239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.296-1.33450.26851190.21442236X-RAY DIFFRACTION79
1.3345-1.37760.21351360.17012728X-RAY DIFFRACTION98
1.3776-1.42680.19651480.14412763X-RAY DIFFRACTION100
1.4268-1.4840.15531430.12632810X-RAY DIFFRACTION100
1.484-1.55150.16381450.12272759X-RAY DIFFRACTION100
1.5515-1.63330.15641480.12612793X-RAY DIFFRACTION100
1.6333-1.73560.18361420.12772798X-RAY DIFFRACTION100
1.7356-1.86960.14791520.13772779X-RAY DIFFRACTION100
1.8696-2.05780.18221500.14632808X-RAY DIFFRACTION100
2.0578-2.35550.15431450.14612814X-RAY DIFFRACTION100
2.3555-2.96740.16631490.15252818X-RAY DIFFRACTION100
2.9674-34.7460.18281480.16542852X-RAY DIFFRACTION100

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