2nu8

C123aT Mutant of E. coli Succinyl-CoA Synthetase

Method: X-RAY DIFFRACTION D_max: 115.4 Å Quality: GOOD

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

Succinyl-CoA ligase [ADP-forming] subunit alpha

Escherichia coli

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–288	Mutation：C123T	Succinyl-CoA synthetase beta chain × 2 （P0A836） PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 4 COA COENZYME A × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.9；294 K；BICINE, Ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.15 Å R-free 0.255
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain D； UniProt 1–288	Mutation：C123T	Succinyl-CoA synthetase beta chain × 2 （P0A836） PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 4 COA COENZYME A × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.9；294 K；BICINE, Ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.15 Å R-free 0.255

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 2NU8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2NU6 C123aA Mutant of E. coli Succinyl-CoA Synthetase Deposited 2006-11-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–288（288 aa）	Mutation：C123A Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 4 COA COENZYME A × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；294 K；BICINE, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.55 Å R-free 0.247
2NU6 C123aA Mutant of E. coli Succinyl-CoA Synthetase Deposited 2006-11-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–288（288 aa）	Mutation：C123A Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 4 COA COENZYME A × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；294 K；BICINE, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.55 Å R-free 0.247
2NU7 C123aS Mutant of E. coli Succinyl-CoA Synthetase Deposited 2006-11-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–288（288 aa）	Mutation：C123S	PO4 PHOSPHATE ION × 2 COA COENZYME A × 6 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；294 K；BICINE, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.20 Å R-free 0.244
2NU7 C123aS Mutant of E. coli Succinyl-CoA Synthetase Deposited 2006-11-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–288（288 aa）	Mutation：C123S	PO4 PHOSPHATE ION × 2 COA COENZYME A × 6 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；294 K；BICINE, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.20 Å R-free 0.244
2NU9 C123aT Mutant of E. coli Succinyl-CoA Synthetase Orthorhombic Crystal Form Deposited 2006-11-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–288（288 aa） Chain F 1–288（288 aa）	Mutation：C123T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C123T Non-standard monomer：Yes (specific site not provided by mmCIF)	COA COENZYME A × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；294 K；BICINE, ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.90 Å R-free 0.251
2NU9 C123aT Mutant of E. coli Succinyl-CoA Synthetase Orthorhombic Crystal Form Deposited 2006-11-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–288（288 aa） Chain H 1–288（288 aa）	Mutation：C123T Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C123T Non-standard monomer：Yes (specific site not provided by mmCIF)	COA COENZYME A × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；294 K；BICINE, ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.90 Å R-free 0.251
2NUA C123aV Mutant of E. coli Succinyl-CoA Synthetase Deposited 2006-11-08	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–288（288 aa）	Mutation：C123V	PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 6 COA COENZYME A × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；294 K；Tris-HCl, ammonium sulfate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.264
2NUA C123aV Mutant of E. coli Succinyl-CoA Synthetase Deposited 2006-11-08	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–288（288 aa）	Mutation：C123V	PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 4 COA COENZYME A × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；294 K；Tris-HCl, ammonium sulfate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.264

4 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SUCD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–288； UniProt 1–288 Author chain D； PDBConstruct 1–288； UniProt 1–288

Succinyl-CoA synthetase beta chain

Escherichia coli

UniProt P0A836

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–388	Not recorded	Succinyl-CoA ligase [ADP-forming] subunit alpha × 2 （P0AGE9） PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 4 COA COENZYME A × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.9；294 K；BICINE, Ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.15 Å R-free 0.255
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 1–388	Not recorded	Succinyl-CoA ligase [ADP-forming] subunit alpha × 2 （P0AGE9） PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 4 COA COENZYME A × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.9；294 K；BICINE, Ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.15 Å R-free 0.255

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 2NU8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JKJ E. coli SCS Deposited 2001-07-12	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–388（388 aa）	Not recorded	PO4 PHOSPHATE ION × 2 COA COENZYME A × 4 GOL GLYCEROL × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.4；294 K；potassium phosphate, ammonium sulfate, pH 7.4, MICRODIALYSIS, temperature 294K	Resolution 2.35 Å R-free 0.238
1JKJ E. coli SCS Deposited 2001-07-12	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–388（388 aa）	Not recorded	PO4 PHOSPHATE ION × 2 COA COENZYME A × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions MICRODIALYSIS；pH 7.4；294 K；potassium phosphate, ammonium sulfate, pH 7.4, MICRODIALYSIS, temperature 294K	Resolution 2.35 Å R-free 0.238
1JLL Crystal Structure Analysis of the E197betaA Mutant of E. coli SCS Deposited 2001-07-16	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–388（388 aa）	Mutation：E197A	PO4 PHOSPHATE ION × 2 COA COENZYME A × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；294 K；Bicine, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.69 Å R-free 0.259
1JLL Crystal Structure Analysis of the E197betaA Mutant of E. coli SCS Deposited 2001-07-16	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–388（388 aa）	Mutation：E197A	PO4 PHOSPHATE ION × 2 COA COENZYME A × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；294 K；Bicine, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.69 Å R-free 0.259
1SCU THE CRYSTAL STRUCTURE OF SUCCINYL-COA SYNTHETASE FROM ESCHERICHIA COLI AT 2.5 ANGSTROMS RESOLUTION Deposited 1993-11-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–388（388 aa） Chain E 1–388（388 aa）	Not recorded	COA COENZYME A × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
2NU6 C123aA Mutant of E. coli Succinyl-CoA Synthetase Deposited 2006-11-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–388（388 aa）	Not recorded	SO4 SULFATE ION × 4 COA COENZYME A × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；294 K；BICINE, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.55 Å R-free 0.247
2NU6 C123aA Mutant of E. coli Succinyl-CoA Synthetase Deposited 2006-11-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–388（388 aa）	Not recorded	SO4 SULFATE ION × 4 COA COENZYME A × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；294 K；BICINE, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.55 Å R-free 0.247
2NU7 C123aS Mutant of E. coli Succinyl-CoA Synthetase Deposited 2006-11-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–388（388 aa）	Not recorded	PO4 PHOSPHATE ION × 2 COA COENZYME A × 6 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；294 K；BICINE, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.20 Å R-free 0.244
2NU7 C123aS Mutant of E. coli Succinyl-CoA Synthetase Deposited 2006-11-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–388（388 aa）	Not recorded	PO4 PHOSPHATE ION × 2 COA COENZYME A × 6 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；294 K；BICINE, ammonium sulfate, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.20 Å R-free 0.244
2NU9 C123aT Mutant of E. coli Succinyl-CoA Synthetase Orthorhombic Crystal Form Deposited 2006-11-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–388（388 aa） Chain G 1–388（388 aa）	Not recorded	COA COENZYME A × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；294 K；BICINE, ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.90 Å R-free 0.251
2NU9 C123aT Mutant of E. coli Succinyl-CoA Synthetase Orthorhombic Crystal Form Deposited 2006-11-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–388（388 aa） Chain I 1–388（388 aa）	Not recorded	COA COENZYME A × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；294 K；BICINE, ammonium sulfate, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.90 Å R-free 0.251
2NUA C123aV Mutant of E. coli Succinyl-CoA Synthetase Deposited 2006-11-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–388（388 aa）	Not recorded	PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 6 COA COENZYME A × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；294 K；Tris-HCl, ammonium sulfate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.264
2NUA C123aV Mutant of E. coli Succinyl-CoA Synthetase Deposited 2006-11-08	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–388（388 aa）	Not recorded	PO4 PHOSPHATE ION × 2 SO4 SULFATE ION × 4 COA COENZYME A × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；294 K；Tris-HCl, ammonium sulfate, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.95 Å R-free 0.264

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

View Construct and Data Evidence

UniProt name	SUCC_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–388； UniProt 1–388 Author chain E； PDBConstruct 1–388； UniProt 1–388

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2nu8
Deposition date deposition_date	2006-11-08
Structure title title	C123aT Mutant of E. coli Succinyl-CoA Synthetase
Keywords keywords	citric acid cycle, heterotetramer, ligase, ATP-GRASP fold, Rossmann fold; LIGASE
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	35.26 Å
Radius of gyration Rg (electron density) rg_electron	35.11 Å
Forward intensity I(0) i0	315324000.00
Molecular weight molecular_weight	144060.0 kDa
Excluded volume excluded_volume	180710 Å³
Envelope volume envelope_volume	216720 Å³
Hydration-shell volume shell_volume	51193 Å³
Envelope diameter envelope_diameter	118.1 Å
Shell Rg shell_rg	41.97 Å
Envelope Rg envelope_rg	34.59 Å
Shape Rg shape_rg	35.12 Å
Total Rg total_rg	35.55 Å
Total atoms total_atoms	10092
Residues n_residues	1347
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	115.4 Å
Rg (real space) rg_real	35.26 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	3.1530e+08
I(0) uncertainty (real space) i0_real_error	4.6650e+06
Rg (reciprocal space) rg_reciprocal	35.27 Å
I(0) (reciprocal space) i0_reciprocal	315300000.0000
Solution quality estimate total_estimate	0.8851
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.5 Å
Skewness Skewness skewness	0.356
Kurtosis Kurtosis kurtosis	-0.396
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	76920000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.885; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.848

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Succinyl-CoA ligase [ADP-forming] subunit alpha
Molecular weight formula_weight	29677.2 kDa
EC 编号 ec_number	6.2.1.5
Mutation mutation	C123T
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	10602

SILIDKNTKVICQGFTGSQGTFHSEQAIAYGTKMVGGVTPGKGGTTHLGLPVFNTVREAVAATGATASVIYVPAPFCKDSILEAIDAGIKLIITITEGIPTLDMLTVKVKLDEAGVRMIGPNTPGVITPGECKIGIQPGHIHKPGKVGIVSRSGTLTYEAVKQTTDYGFGQSTCVGIGGDPIPGSNFIDILEMFEKDPQTEAIVMIGEIGGSAEEEAAAYIKEHVTKPVVGYIAGVTAPKGKRMGHAGAIIAGGKGTADEKFAALEAAGVKTVRSLADIGEALKTVLK

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Succinyl-CoA synthetase beta chain
Molecular weight formula_weight	41438.5 kDa
EC 编号 ec_number	6.2.1.5
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MNLHEYQAKQLFARYGLPAPVGYACTTPREAEEAASKIGAGPWVVKCQVHAGGRGKAGGVKVVNSKEDIRAFAENWLGKRLVTYQTDANGQPVNQILVEAATDIAKELYLGAVVDRSSRRVVFMASTEGGVEIEKVAEETPHLIHKVALDPLTGPMPYQGRELAFKLGLEGKLVQQFTKIFMGLATIFLERDLALIEINPLVITKQGDLICLDGKLGADGNALFRQPDLREMRDQSQEDPREAQAAQWELNYVALDGNIGCMVNGAGLAMGTMDIVKLHGGEPANFLDVGGGATKERVTEAFKIILSDDKVKAVLVNIFGGIVRCDLIADGIIGAVAEVGVNVPVVVRLEGNNAELGAKKLADSGLNIIAAKGLTDAAQQVVAAVEGK

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	510

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7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2nu8a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.8 — CoA-binding domain

Domain ID domain_id	d2nu8a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.4 — Succinyl-CoA synthetase domains
Family Family family	c.23.4.1 — Succinyl-CoA synthetase domains

Domain ID domain_id	d2nu8b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.4 — Succinyl-CoA synthetase domains
Family Family family	c.23.4.1 — Succinyl-CoA synthetase domains

Domain ID domain_id	d2nu8b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family family	d.142.1.4 — Succinyl-CoA synthetase, beta-chain, N-terminal domain

Domain ID domain_id	d2nu8d1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.8 — CoA-binding domain

Domain ID domain_id	d2nu8d2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.4 — Succinyl-CoA synthetase domains
Family Family family	c.23.4.1 — Succinyl-CoA synthetase domains

Domain ID domain_id	d2nu8e1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.4 — Succinyl-CoA synthetase domains
Family Family family	c.23.4.1 — Succinyl-CoA synthetase domains

Domain ID domain_id	d2nu8e2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.142 — ATP-grasp
Superfamily Superfamily superfamily	d.142.1 — Glutathione synthetase ATP-binding domain-like
Family Family family	d.142.1.4 — Succinyl-CoA synthetase, beta-chain, N-terminal domain

CATH v4.4 (10 domains)

Domain ID domain_id	2nu8A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2nu8A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	261 — Succinyl-CoA synthetase domains

Domain ID domain_id	2nu8B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, B domain

Domain ID domain_id	2nu8B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, A domain

Domain ID domain_id	2nu8B03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	261 — Succinyl-CoA synthetase domains

Domain ID domain_id	2nu8D01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2nu8D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	261 — Succinyl-CoA synthetase domains

Domain ID domain_id	2nu8E01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	470 — D-amino Acid Aminotransferase; Chain A, domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, B domain

Domain ID domain_id	2nu8E02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	20 — ATP-grasp fold, A domain

Domain ID domain_id	2nu8E03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	261 — Succinyl-CoA synthetase domains

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8. Citations (1)

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Unit-cell length a length_a	96.690 Å
Unit-cell length b length_b	96.690 Å
Unit-cell length c length_c	385.940 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	16

Space group space_group	P 43 2 2
Space-group number int_tables_number	95
Crystal system crystal_system	—

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	41.970 Å
R factor r_factor	0.2150
R_work r_work	0.2100
R_free r_free	0.2550

fit	/app/data/saxs_computation/nu/2nu8/2nu8.fit
pddf	/app/data/pr_computation/nu/2nu8/2nu8.pr.out
profile	/app/data/saxs_computation/nu/2nu8/2nu8.dat

C123aT Mutant of E. coli Succinyl-CoA Synthetase

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

Succinyl-CoA ligase [ADP-forming] subunit alpha

State in the Current Structure

Other States of the Same Protein in the Database

Succinyl-CoA synthetase beta chain

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

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)