SAXSdb — 6cts

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

CITRATE SYNTHASE

Gallus gallus

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 1–433	Not recorded	CIC CITRYL-THIOETHER-COENZYME *A × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.50 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 6CTS	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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 mutation/modification Different ligand/ion 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 ligand/ion 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
6CSC CHICKEN CITRATE SYNTHASE COMPLEX WITH TRIFLUOROACETONYL-COA AND CITRATE 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 1–429（429 aa） Chain B 1–429（429 aa）	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

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 1–433

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	6cts
Deposition date deposition_date	1989-11-16
Structure title title	PROPOSED MECHANISM FOR THE CONDENSATION REACTION OF CITRATE SYNTHASE. 1.9-ANGSTROMS STRUCTURE OF THE TERNARY COMPLEX WITH OXALOACETATE AND CARBOXYMETHYL COENZYME A
Keywords keywords	OXO-ACID-LYASE; 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	22.94 Å
Radius of gyration Rg (electron density) rg_electron	21.78 Å
Forward intensity I(0) i0	38064800.00
Molecular weight molecular_weight	47846.0 kDa
Excluded volume excluded_volume	59988 Å³
Envelope volume envelope_volume	71378 Å³
Hydration-shell volume shell_volume	26589 Å³
Envelope diameter envelope_diameter	74.7 Å
Shell Rg shell_rg	29.58 Å
Envelope Rg envelope_rg	22.33 Å
Shape Rg shape_rg	21.76 Å
Total Rg total_rg	22.78 Å
Total atoms total_atoms	3365
Residues n_residues	429
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	73.3 Å
Rg (real space) rg_real	22.83 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	3.8060e+07
I(0) uncertainty (real space) i0_real_error	4.9020e+05
Rg (reciprocal space) rg_reciprocal	22.86 Å
I(0) (reciprocal space) i0_reciprocal	38070000.0000
Solution quality estimate total_estimate	0.8924
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.2 Å
Skewness Skewness skewness	0.216
Kurtosis Kurtosis kurtosis	-0.402
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8053000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.955

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	CITRATE SYNTHASE
Molecular weight formula_weight	47322.2 kDa
EC 编号 ec_number	4.1.3.7
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3466

ASSTNLKDVLAALIPKEQARIKTFRQQHGGTALGQITVDMSYGGMRGMKGLVYETSVLDPDEGIRFRGFSIPECQKLLPKGGXGGEPLPEGLFWLLVTGQIPTGAQVSWLSKEWAKRAALPSHVVTMLDNFPTNLHPMSQLSAAITALNSESNFARAYAEGILRTKYWEMVYESAMDLIAKLPCVAAKIYRNLYRAGSSIGAIDSKLDWSHNFTNMLGYTDAQFTELMRLYLTIHSDHEGGNVSAHTSHLVGSALSDPYLSFAAAMNGLAGPLHGLANQEVLGWLAQLQKAXXXAGADASLRDYIWNTLNSGRVVPGYGHAVLRKTDPRYTCQREFALKHLPGDPMFKLVAQLYKIVPNVLLEQGAAANPWPNVDAHSGVLLQYYGMTEMNYYTVLFGVSRALGVLAQLIWSRALGFPLERPKSMSTDGLIAL

来源 Source

来源生物 organism	Gallus gallus
通用名 common_name	chicken
NCBI Class编号 ncbi_taxonomy_id	9031

Entity 2 Entity 2 non-polymer

Description description	CITRYL-THIOETHER-COENZYME *A
Molecular weight formula_weight	927.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	101

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6ctsa_
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 (2 domains)

Domain ID domain_id	6ctsA01
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	6ctsA02
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 (5)

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Unit-cell length a length_a	104.000 Å
Unit-cell length b length_b	78.100 Å
Unit-cell length c length_c	58.300 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	78.90 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1100
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/ct/6cts/6cts.fit
pddf	/app/data/pr_computation/ct/6cts/6cts.pr.out
profile	/app/data/saxs_computation/ct/6cts/6cts.dat

PROPOSED MECHANISM FOR THE CONDENSATION REACTION OF CITRATE SYNTHASE. 1.9-ANGSTROMS STRUCTURE OF THE TERNARY COMPLEX WITH OXALOACETATE AND CARBOXYMETHYL COENZYME A

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