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- PDB-1css: ALPHA-FLUORO ACID AND ALPHA-FLUORO AMIDE ANALOGS OF ACETYL-COA AS... -

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Basic information

Entry
Database: PDB / ID: 1css
TitleALPHA-FLUORO ACID AND ALPHA-FLUORO AMIDE ANALOGS OF ACETYL-COA AS INHIBITORS OF OF CITRATE SYNTHASE: EFFECT OF PKA MATCHING ON BINDING AFFINITY AND HYDROGEN BOND LENGTH
ComponentsCITRATE SYNTHASE
KeywordsOXO-ACID-LYASE
Function / homology
Function and homology information


The tricarboxylic acid cycle / citrate (Si)-synthase / citrate synthase activity / : / citrate metabolic process / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix / mitochondrion / identical protein binding
Similarity search - Function
Citrate synthase, eukaryotic-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain ...Citrate synthase, eukaryotic-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-FCX / OXALOACETATE ION / Citrate synthase, mitochondrial
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsUsher, K.C. / Remington, S.J.
Citation
Journal: Biochemistry / Year: 1995
Title: alpha-Fluoro acid and alpha-fluoro amide analogs of acetyl-CoA as inhibitors of citrate synthase: effect of pKa matching on binding affinity and hydrogen bond length.
Authors: Schwartz, B. / Drueckhammer, D.G. / Usher, K.C. / Remington, S.J.
#1: Journal: Biochemistry / Year: 1994
Title: A Very Short Hydrogen Bond Provides Only Moderate Stabilization of an Enzyme-Inhibitor Complex of Citrate Synthase
Authors: Usher, K.C. / Remington, S.J. / Martin, D.P. / Drueckhammer, D.G.
#2: Journal: Biochemistry / Year: 1990
Title: Proposed Mechanism for the Condensation Reaction of Citrate Synthase: 1.9-Angstroms Structure of the Ternary Complex with Oxaloacetate and Carboxymethyl Coenzyme A
Authors: Karpusas, M. / Branchaud, B. / Remington, S.J.
#3: Journal: J.Mol.Biol. / Year: 1984
Title: Crystal Structure Analysis and Molecular Model of a Complex of Citrate Synthase with Oxaloacetate and S-Acetonyl-Coenzyme A
Authors: Wiegand, G. / Remington, S. / Deisenhofer, J. / Huber, R.
#4: Journal: J.Mol.Biol. / Year: 1982
Title: Crystallographic Refinement and Atomic Models of Two Different Forms of Citrate Synthase at 2.7 And 1.7 Angstroms Resolution
Authors: Remington, S. / Wiegand, G. / Huber, R.
History
DepositionAug 4, 1995Processing site: BNL
Revision 1.0Oct 15, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

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Assembly

Deposited unit
A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1173
Polymers48,1751
Non-polymers9432
Water2,612145
1
A: CITRATE SYNTHASE
hetero molecules

A: CITRATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,2356
Polymers96,3502
Non-polymers1,8854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13590 Å2
ΔGint-40 kcal/mol
Surface area28070 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)104.390, 78.430, 58.470
Angle α, β, γ (deg.)90.00, 78.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CITRATE SYNTHASE


Mass: 48174.934 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Organ: HEART / Tissue: MUSCLE / References: UniProt: P23007, EC: 4.1.3.7
#2: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#3: Chemical ChemComp-FCX / ALPHA-FLUORO-CARBOXYMETHYLDETHIA COENZYME A COMPLEX


Mass: 811.496 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H37FN7O18P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 mMenzyme1drop
20.5 Mcitrate1drop

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Data collection

Diffraction sourceWavelength: 1.54
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Dec 15, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionRedundancy: 1.8 % / Rmerge(I) obs: 0.044
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 25 Å / Num. obs: 44220 / % possible obs: 86 % / Observed criterion σ(I): 0 / Num. measured all: 77964 / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 2 Å / % possible obs: 74 %

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Processing

SoftwareName: TNT / Classification: refinement
RefinementResolution: 1.7→25 Å / σ(F): 0 /
RfactorNum. reflection% reflection
obs0.165 44220 86 %
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3391 0 61 145 3597
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg2.8
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.009
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd

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