SAXSdb — 6csc

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1. Protein Identity and Related Structures Protein Identity & Related Structures

CITRATE SYNTHASE

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–429 Chain B； UniProt 1–429	Not recorded	COF TRIFLUOROACETONYL COENZYME A × 2 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6；CRYSTALLIZED FROM 1.05M NA CITRATE, PH 6.0 2 MM TRIFLUOROACETONYL COENZYME A	Resolution 2.25 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 6CSC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AL6 CHICKEN CITRATE SYNTHASE COMPLEX WITH N-HYDROXYAMIDO-COA AND OXALOACETATE Deposited 1997-06-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–429（429 aa）	Not recorded	OAA OXALOACETATE ION × 2 HAX N-HYDROXYAMIDOCARBOXYMETHYLDETHIA COENZYME *A × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；CRYSTALLIZED FROM 1.02M NA CITRATE, PH 6.0 5 MM OXALOACETATE, PH 6 2 MM N-HYDROXYAMIDOCARBOXYMETHYLDETHIA COENZYME A.	Resolution 1.85 Å
1AMZ CHICKEN CITRATE SYNTHASE COMPLEX WITH NITROMETHYLDE-COA AND MALATE Deposited 1997-06-19	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–429（427 aa）	Not recorded	MLT D-MALATE × 2 NMX NITROMETHYLDETHIA COENZYME A × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；CRYSTALLIZED FROM 1.01M NA MALATE, PH 6.0 2 MM NITROMETHYLDETHIA COENZYME A THE CELL ANGLE BETA IS DEFINED AS THE ACUTE ANGLE FOR CONSISTENCY WITH PREVIOUS PDB ENTRIES OF CITRATE SYNTHASE IN THIS SPACE GROUP	Resolution 1.80 Å
1CSC Structure of ternary complexes of citrate synthase with D-and L-malate: Mechanistic implications Deposited 1990-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–433（433 aa）	Not recorded	CMC CARBOXYMETHYL COENZYME A × 2 LMR* (2S)-2-hydroxybutanedioic acid × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
1CSH A very short hydrogen bond provides only moderate stabilization of an enzyme: inhibitor complex of citrate synthase Deposited 1994-03-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–460（431 aa）	Not recorded	OAA OXALOACETATE ION × 2 AMX AMIDOCARBOXYMETHYLDETHIA COENZYME *A × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.65 Å
1CSI A very short hydrogen bond provides only moderate stabilization of an enzyme: inhibitor complex of citrate synthase Deposited 1994-03-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–460（431 aa）	Not recorded	OAA OXALOACETATE ION × 2 CMX CARBOXYMETHYLDETHIA COENZYME *A × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
1CSR Alpha-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 Deposited 1995-08-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–460（431 aa）	Not recorded	OAA OXALOACETATE ION × 2 FAM ALPHA-FLUORO-AMIDOCARBOXYMETHYLDETHIA COENZYME A COMPLEX × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
1CSS ALPHA-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 Deposited 1995-08-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 30–460（431 aa）	Not recorded	OAA OXALOACETATE ION × 2 FCX ALPHA-FLUORO-CARBOXYMETHYLDETHIA COENZYME A COMPLEX × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
2CSC Structure of ternary complexes of CITRATE SYNTHASE WITH D-AND L-MALATE: mechanistic implications Deposited 1990-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–433（433 aa）	Not recorded	CMC CARBOXYMETHYL COENZYME A × 2 MLT* D-MALATE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
3CSC STRUCTURE OF TERNARY COMPLEXES OF CITRATE SYNTHASE WITH D-AND L-MALATE: MECHANISTIC IMPLICATIONS Deposited 1990-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–433（433 aa）	Not recorded	ACO ACETYL COENZYME A × 2 LMR* (2S)-2-hydroxybutanedioic acid × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
4CSC STRUCTURE OF TERNARY COMPLEXES OF CITRATE SYNTHASE WITH D-AND L-MALATE: MECHANISTIC IMPLICATIONS Deposited 1990-05-07	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–433（433 aa）	Not recorded	MLT D-MALATE × 2 ACO ACETYL COENZYME *A × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
5CSC STRUCTURE OF AN OPEN FORM OF CHICKEN HEART CITRATE SYNTHASE AT 2.8 ANGSTROMS RESOLUTION Deposited 1990-05-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–433（433 aa） Chain B 1–433（433 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
5CTS PROPOSED MECHANISM FOR THE CONDENSATION REACTION OF CITRATE SYNTHASE. 1.9-ANGSTROMS STRUCTURE OF THE TERNARY COMPLEX WITH OXALOACETATE AND CARBOXYMETHYL COENZYME A Deposited 1989-11-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–433（433 aa）	Not recorded	OAA OXALOACETATE ION × 2 CMC CARBOXYMETHYL COENZYME *A × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
6CTS PROPOSED MECHANISM FOR THE CONDENSATION REACTION OF CITRATE SYNTHASE. 1.9-ANGSTROMS STRUCTURE OF THE TERNARY COMPLEX WITH OXALOACETATE AND CARBOXYMETHYL COENZYME A Deposited 1989-11-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–433（433 aa）	Not recorded	CIC CITRYL-THIOETHER-COENZYME *A × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CISY_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–433； UniProt 1–429 Author chain B； PDBConstruct 1–433； UniProt 1–429

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6csc
Deposition date deposition_date	1997-06-19
Structure title title	CHICKEN CITRATE SYNTHASE COMPLEX WITH TRIFLUOROACETONYL-COA AND CITRATE
Keywords keywords	OXO-ACID-LYASE, TRICARBOXYLIC ACID CYCLE, ALLOSTERIC ENZYME; OXO-ACID-LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	27.61 Å
Radius of gyration Rg (electron density) rg_electron	26.63 Å
Forward intensity I(0) i0	153234000.00
Molecular weight molecular_weight	98421.0 kDa
Excluded volume excluded_volume	123190 Å³
Envelope volume envelope_volume	138780 Å³
Hydration-shell volume shell_volume	41204 Å³
Envelope diameter envelope_diameter	93.7 Å
Shell Rg shell_rg	35.83 Å
Envelope Rg envelope_rg	26.87 Å
Shape Rg shape_rg	26.64 Å
Total Rg total_rg	27.43 Å
Total atoms total_atoms	6923
Residues n_residues	871
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	88.9 Å
Rg (real space) rg_real	27.43 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	1.5320e+08
I(0) uncertainty (real space) i0_real_error	2.1220e+06
Rg (reciprocal space) rg_reciprocal	27.49 Å
I(0) (reciprocal space) i0_reciprocal	153200000.0000
Solution quality estimate total_estimate	0.8880
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.3 Å
Skewness Skewness skewness	0.202
Kurtosis Kurtosis kurtosis	-0.378
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	51470000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.852; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.994

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	CITRATE SYNTHASE
Molecular weight formula_weight	48333.1 kDa
EC 编号 ec_number	4.1.3.7
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	7101

ASSTNLKDVLASLIPKEQARIKTFRQQHGNTAVGQITVDMSYGGMRGMKGLIYETSVLDPDEGIRFRGFSIPECQKLLPKAGGGEEPLPEGLFWLLVTGQIPTPEQVSWVSKEWAKRAALPSHVVTMLDNFPTNLHPMSQLSAAITALNSESNFARAYAEGINRTKYWEFVYEDAMDLIAKLPCVAAKIYRNLYRAGSSIGAIDSKLDWSHNFTNMLGYTDPQFTELMRLYLTIHSDHEGGNVSAHTSHLVGSALSDPYLSFAAAMNGLAGPLHGLANQEVLLWLSQLQKDLGADASDEKLRDYIWNTLNSGRVVPGYGHAVLRKTDPRYTCQREFALKHLPSDPMFKLVAQLYKIVPNVLLEQGKAKNPWPNVDAHSGVLLQYYGMTEMNYYTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTAGLEKLSAGG

Entity 2 Entity 2 non-polymer

Description description	TRIFLUOROACETONYL COENZYME A
Molecular weight formula_weight	877.6 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6csca_
Class class	a — All alpha proteins
Fold Fold fold	a.103 — Citrate synthase
Superfamily Superfamily superfamily	a.103.1 — Citrate synthase
Family Family family	a.103.1.1 — Citrate synthase

Domain ID domain_id	d6cscb_
Class class	a — All alpha proteins
Fold Fold fold	a.103 — Citrate synthase
Superfamily Superfamily superfamily	a.103.1 — Citrate synthase
Family Family family	a.103.1.1 — Citrate synthase

CATH v4.4 (4 domains)

Domain ID domain_id	6cscA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	580 — Citrate Synthase; domain 1
Homologous superfamily homologous superfamily	10 — Citrate Synthase, domain 1

Domain ID domain_id	6cscA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	230 — Cytochrome p450-Terp; domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome P450-Terp, domain 2

Domain ID domain_id	6cscB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	580 — Citrate Synthase; domain 1
Homologous superfamily homologous superfamily	10 — Citrate Synthase, domain 1

Domain ID domain_id	6cscB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	230 — Cytochrome p450-Terp; domain 2
Homologous superfamily homologous superfamily	10 — Cytochrome P450-Terp, domain 2

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8. Citations (4)

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Unit-cell length a length_a	110.370 Å
Unit-cell length b length_b	100.210 Å
Unit-cell length c length_c	87.840 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.1580
R_free r_free	—

fit	/app/data/saxs_computation/cs/6csc/6csc.fit
pddf	/app/data/pr_computation/cs/6csc/6csc.pr.out
profile	/app/data/saxs_computation/cs/6csc/6csc.dat

CHICKEN CITRATE SYNTHASE COMPLEX WITH TRIFLUOROACETONYL-COA AND CITRATE

1. Protein Identity and Related Structures Protein Identity & Related Structures

CITRATE SYNTHASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction