SAXSdb — 1c3a

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

FLAVOCETIN-A: ALPHA SUBUNIT

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 heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 24–158	Not recorded	FLAVOCETIN-A: BETA SUBUNIT × 4 （Q8AV98）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2-methyl-2,4-pentanediol, calcium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.269
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 24–158	Not recorded	FLAVOCETIN-A: BETA SUBUNIT × 1 （Q8AV98）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2-methyl-2,4-pentanediol, calcium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.269

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q8AV97_TRIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–135； UniProt 24–158

FLAVOCETIN-A: BETA SUBUNIT

OrganismNot specified

UniProt Q8AV98

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain B； UniProt 24–148	Not recorded	FLAVOCETIN-A: ALPHA SUBUNIT × 4 （Q8AV97）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2-methyl-2,4-pentanediol, calcium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.269
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 24–148	Not recorded	FLAVOCETIN-A: ALPHA SUBUNIT × 1 （Q8AV97）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2-methyl-2,4-pentanediol, calcium chloride, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.50 Å R-free 0.269

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q8AV98_TRIFL
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–125； UniProt 24–148

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	1c3a
Deposition date deposition_date	1999-07-27
Structure title title	CRYSTAL STRUCTURE OF FLAVOCETIN-A FROM THE HABU SNAKE VENOM, A NOVEL CYCLIC TETRAMER OF C-TYPE LECTIN-LIKE HETERODIMERS
Keywords keywords	C-TYPE LECTIN-LIKE DOMAINS, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	22.97 Å
Radius of gyration Rg (electron density) rg_electron	22.56 Å
Forward intensity I(0) i0	16475900.00
Molecular weight molecular_weight	30190.0 kDa
Excluded volume excluded_volume	37393 Å³
Envelope volume envelope_volume	44752 Å³
Hydration-shell volume shell_volume	17796 Å³
Envelope diameter envelope_diameter	84.9 Å
Shell Rg shell_rg	27.67 Å
Envelope Rg envelope_rg	23.09 Å
Shape Rg shape_rg	22.53 Å
Total Rg total_rg	23.33 Å
Total atoms total_atoms	2124
Residues n_residues	260
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	82.7 Å
Rg (real space) rg_real	23.22 Å
Rg uncertainty (real space) rg_real_error	0.82 Å
I(0) (real space) i0_real	1.6480e+07
I(0) uncertainty (real space) i0_real_error	2.4470e+05
Rg (reciprocal space) rg_reciprocal	23.16 Å
I(0) (reciprocal space) i0_reciprocal	16480000.0000
Solution quality estimate total_estimate	0.7731
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.6 Å
Skewness Skewness skewness	0.591
Kurtosis Kurtosis kurtosis	-0.246
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6254000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.510; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.562; 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	FLAVOCETIN-A: ALPHA SUBUNIT
Molecular weight formula_weight	15667.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2217

DFDCIPGWSAYDRYCYQAFSKPKNWEDAESFCEEGVKTSHLVSIESSGEGDFVAQLVAEKIKTSFQYVWIGLRIQNKEQQCRSEWSDASSVNYENLVKQFSKKCYALKKGTELRTWFNVYCGTENPEVCKYTPEC

Entity 2 Entity 2 polymer

Description description	FLAVOCETIN-A: BETA SUBUNIT
Molecular weight formula_weight	14563.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GFCCPLGWSSYDEHCYQVFQQKMNWEDAEKFCTQQHKGSHLVSFHSSEEVDFVTSKTFPILKYDFVWIGLSNVWNECTKEWSDGTKLDYKAWSGGSDCIVSKTTDNQWLSMDCSSKYYVVCKFQA

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	93

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1c3aa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

Domain ID domain_id	d1c3ab_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.1 — C-type lectin domain

CATH v4.4 (2 domains)

Domain ID domain_id	1c3aA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1c3aB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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8. Citations (1)

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Unit-cell length a length_a	120.510 Å
Unit-cell length b length_b	120.510 Å
Unit-cell length c length_c	62.840 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	I 4
Space-group number int_tables_number	79
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2690

fit	/app/data/saxs_computation/c3/1c3a/1c3a.fit
pddf	/app/data/pr_computation/c3/1c3a/1c3a.pr.out
profile	/app/data/saxs_computation/c3/1c3a/1c3a.dat

CRYSTAL STRUCTURE OF FLAVOCETIN-A FROM THE HABU SNAKE VENOM, A NOVEL CYCLIC TETRAMER OF C-TYPE LECTIN-LIKE HETERODIMERS

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

FLAVOCETIN-A: ALPHA SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

FLAVOCETIN-A: BETA SUBUNIT

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)