SAXSdb — 2vk5

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

EXO-ALPHA-SIALIDASE

CLOSTRIDIUM PERFRINGENS

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 243–694	Fragment：CATALYTIC DOMAIN, RESIDUES 243-694	GOL GLYCEROL × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 0.97 Å R-free 0.126

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 2VK5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2BF6 Atomic Resolution Structure of the bacterial sialidase NanI from Clostridium perfringens in complex with alpha-Sialic Acid (Neu5Ac). Deposited 2004-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 243–691（449 aa） Fragment：RESIDUES 243-691	Not recorded	SIA N-acetyl-alpha-neuraminic acid × 1 CA CALCIUM ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；20 % PEG 3350, 0.2M POTASSIUM NITRATE, pH 7.00	Resolution 0.97 Å R-free 0.133
2VK6 THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES Deposited 2007-12-17	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 243–694（452 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 243-694	Not recorded	CA CALCIUM ION × 1 DAN 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID × 1 MG MAGNESIUM ION × 4 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å R-free 0.185
2VK7 THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES Deposited 2007-12-17	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 243–694（452 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 243-694	Not recorded	CA CALCIUM ION × 2 FSI 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.20 Å R-free 0.159
2VK7 THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES Deposited 2007-12-17	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 243–694（452 aa） Fragment：CATALYTIC DOMAIN, RESIDUES 243-694	Not recorded	CA CALCIUM ION × 2 FSI 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.20 Å R-free 0.159
8XQL Structure of human class T GPCR TAS2R14-miniGs/gust complex with Aristolochic acid A. Deposited 2024-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 243–694（452 aa）	Not recorded	GOQ 8-methoxy-6-nitro-naphtho[1,2-e][1,3]benzodioxole-5-carboxylic acid × 2 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.99 Å
8XQN Structure of human class T GPCR TAS2R14-DNGi complex with Aristolochic acid A. Deposited 2024-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 243–694（452 aa）	Not recorded	GOQ 8-methoxy-6-nitro-naphtho[1,2-e][1,3]benzodioxole-5-carboxylic acid × 1 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å
8XQO Structure of human class T GPCR TAS2R14-Gi complex with Aristolochic acid A. Deposited 2024-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 243–694（452 aa）	Not recorded	GOQ 8-methoxy-6-nitro-naphtho[1,2-e][1,3]benzodioxole-5-carboxylic acid × 1 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.77 Å
8XQP Structure of human class T GPCR TAS2R14-Gustducin complex with Aristolochic acid A. Deposited 2024-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 243–694（452 aa）	Not recorded	GOQ 8-methoxy-6-nitro-naphtho[1,2-e][1,3]benzodioxole-5-carboxylic acid × 1 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
8XQS Structure of human class T GPCR TAS2R14-DNGi complex with Flufenamic acid. Deposited 2024-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 243–694（452 aa）	Not recorded	FLF 2-[[3-(TRIFLUOROMETHYL)PHENYL]AMINO] BENZOIC ACID × 1 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8XQT Structure of human class T GPCR TAS2R14-Gi complex. Deposited 2024-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 243–694（452 aa）	Not recorded	CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.94 Å
8XVE Cryo-EM structure of ETBR bound with BQ3020 Deposited 2024-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 243–694（452 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8XVH Cryo-EM structure of ETBR bound with Endothelin1 Deposited 2024-01-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 243–694（452 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.26 Å
8YKY Structure of human class T GPCR TAS2R14-Ggustducin complex with agonist 28.1 Deposited 2024-03-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 243–694（452 aa）	Not recorded	A1AEI 4-methyl-N-[(2M)-2-(1H-tetrazol-5-yl)phenyl]-6-(trifluoromethyl)pyrimidin-2-amine × 1 CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.99 Å

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

View Construct and Data Evidence

UniProt name	Q59310_CLOPE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–452； UniProt 243–694

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	2vk5
Deposition date deposition_date	2007-12-17
Structure title title	THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES
Keywords keywords	HYDROLASE, SIALIDASE, GLYCOSIDASE, SIALIC ACID, CLOSTRIDIUM PERFRINGENS; HYDROLASE
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	22.88 Å
Radius of gyration Rg (electron density) rg_electron	21.85 Å
Forward intensity I(0) i0	42894800.00
Molecular weight molecular_weight	50231.0 kDa
Excluded volume excluded_volume	62504 Å³
Envelope volume envelope_volume	71212 Å³
Hydration-shell volume shell_volume	26701 Å³
Envelope diameter envelope_diameter	82.9 Å
Shell Rg shell_rg	29.44 Å
Envelope Rg envelope_rg	22.27 Å
Shape Rg shape_rg	21.83 Å
Total Rg total_rg	22.73 Å
Total atoms total_atoms	3538
Residues n_residues	449
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	80.4 Å
Rg (real space) rg_real	22.81 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	4.2890e+07
I(0) uncertainty (real space) i0_real_error	6.1760e+05
Rg (reciprocal space) rg_reciprocal	22.83 Å
I(0) (reciprocal space) i0_reciprocal	42900000.0000
Solution quality estimate total_estimate	0.8504
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	79.2 Å
Skewness Skewness skewness	0.321
Kurtosis Kurtosis kurtosis	-0.138
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13620000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.687; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.995

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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	EXO-ALPHA-SIALIDASE
Molecular weight formula_weight	50405.9 kDa
EC 编号 ec_number	3.2.1.18
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	4628

VEGAVKTEPVDLFHPGFLNSSNYRIPALFKTKEGTLIASIDARRHGGADAPNNDIDTAVRRSEDGGKTWDEGQIIMDYPDKSSVIDTTLIQDDETGRIFLLVTHFPSKYGFWNAGLGSGFKNIDGKEYLCLYDSSGKEFTVRENVVYDKDSNKTEYTTNALGDLFKNGTKIDNINSSTAPLKAKGTSYINLVYSDDDGKTWSEPQNINFQVKKDWMKFLGIAPGRGIQIKNGEHKGRIVVPVYYTNEKGKQSSAVIYSDDSGKNWTIGESPNDNRKLENGKIINSKTLSDDAPQLTECQVVEMPNGQLKLFMRNLSGYLNIATSFDGGATWDETVEKDTNVLEPYCQLSVINYSQKVDGKDAVIFSNPNARSRSNGTVRIGLINQVGTYENGEPKYEFDWKYNKLVKPGYYAYSCLTELSNGNIGLLYEGTPSEEMSYIEMNLKYLESGANK

来源 Source

来源生物 organism	CLOSTRIDIUM PERFRINGENS
NCBI Class编号 ncbi_taxonomy_id	1502
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 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	1030

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2vk5A01
Class class	2 — Mainly Beta
Architecture architecture	120 — 6 Propeller
Topology topology	10 — Neuraminidase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2vk5A02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	220 — Intramolecular trans-sialidase; domain 3
Homologous superfamily homologous superfamily	10 — Intramolecular Trans-sialidase; Domain 3

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8. Citations (1)

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Unit-cell length a length_a	96.892 Å
Unit-cell length b length_b	69.019 Å
Unit-cell length c length_c	72.808 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	4

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

Resolution resolution	0.970 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.1150
R_free r_free	0.1260

fit	/app/data/saxs_computation/vk/2vk5/2vk5.fit
pddf	/app/data/pr_computation/vk/2vk5/2vk5.pr.out
profile	/app/data/saxs_computation/vk/2vk5/2vk5.dat

THE STRUCTURE OF CLOSTRIDIUM PERFRINGENS NANI SIALIDASE AND ITS CATALYTIC INTERMEDIATES

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

EXO-ALPHA-SIALIDASE

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