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- PDB-1rri: DHNA complex with 3-(5-amino-7-hydroxy-[1,2,3] triazolo [4,5-d]py... -

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Basic information

Entry
Database: PDB / ID: 1rri
TitleDHNA complex with 3-(5-amino-7-hydroxy-[1,2,3] triazolo [4,5-d]pyrimidin-2-yl)-benzoic acid
ComponentsDihydroneopterin aldolase
KeywordsLYASE / DHNA complex with 3-(5-amino-7-hydroxy-[1 / 2 / 3] triazolo [4 / 5-d]pyrimidin-2-yl)-benzoic acid
Function / homology
Function and homology information


7,8-dihydroneopterin epimerase / dihydroneopterin aldolase / dihydroneopterin aldolase activity / folic acid biosynthetic process / isomerase activity / tetrahydrofolate biosynthetic process / cytoplasm
Similarity search - Function
Dihydroneopterin aldolase / Dihydroneopterin aldolase/epimerase domain / Dihydroneopterin aldolase / Dihydroneopterin aldolase / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-A45 / Dihydroneopterin aldolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSanders, W.J. / Nienaber, V.L. / Lerner, C.G. / McCall, J.O. / Merrick, S.M. / Swanson, S.J. / Harlan, J.E. / Stoll, V.S. / Stamper, G.F. / Betz, S.F. ...Sanders, W.J. / Nienaber, V.L. / Lerner, C.G. / McCall, J.O. / Merrick, S.M. / Swanson, S.J. / Harlan, J.E. / Stoll, V.S. / Stamper, G.F. / Betz, S.F. / Condroski, K.R. / Meadows, R.P. / Severin, J.M. / Walter, K.A. / Magdalinos, P. / Jakob, C.G. / Wagner, R. / Beutel, B.A.
CitationJournal: J.Med.Chem. / Year: 2004
Title: Discovery of Potent Inhibitors of Dihydroneopterin Aldolase Using CrystaLEAD High-Throughput X-ray Crystallographic Screening and Structure-Directed Lead Optimization.
Authors: Sanders, W.J. / Nienaber, V.L. / Lerner, C.G. / McCall, J.O. / Merrick, S.M. / Swanson, S.J. / Harlan, J.E. / Stoll, V.S. / Stamper, G.F. / Betz, S.F. / Condroski, K.R. / Meadows, R.P. / ...Authors: Sanders, W.J. / Nienaber, V.L. / Lerner, C.G. / McCall, J.O. / Merrick, S.M. / Swanson, S.J. / Harlan, J.E. / Stoll, V.S. / Stamper, G.F. / Betz, S.F. / Condroski, K.R. / Meadows, R.P. / Severin, J.M. / Walter, K.A. / Magdalinos, P. / Jakob, C.G. / Wagner, R. / Beutel, B.A.
History
DepositionDec 8, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Dihydroneopterin aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0422
Polymers13,7701
Non-polymers2721
Water00
1
A: Dihydroneopterin aldolase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)112,33516
Polymers110,1578
Non-polymers2,1788
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area26600 Å2
ΔGint-120 kcal/mol
Surface area36060 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.947, 60.947, 123.689
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Dihydroneopterin aldolase / DHNA


Mass: 13769.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: FOLB / Production host: Escherichia coli (E. coli) / References: UniProt: P56740, dihydroneopterin aldolase
#2: Chemical ChemComp-A45 / 3-(5-AMINO-7-HYDROXY-[1,2,3]TRIAZOLO[4,5-D]PYRIMIDIN-2-YL)-BENZOIC ACID


Mass: 272.220 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8N6O3

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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: 2.08 Å3/Da / Density % sol: 41.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M Ammonium Acetate, 0.1M tri-sodium citrate pH 5.6, 30% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→20.05 Å / Num. obs: 6827 / % possible obs: 82.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.13 Å / % possible all: 78

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR98refinement
HKL-2000data reduction
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→20.05 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.316 726 10.6
Rwork0.265 --
obs-6827 -
Refine analyzeLuzzati coordinate error obs: 0.4 Å / Luzzati sigma a obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2→20.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms967 0 20 0 987
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.75

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