SAXSdb — 1clp

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

MYOTOXIN II

Bothrops asper

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 1–121	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.80 Å
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–121	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.80 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 1CLP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1Y4L Crystal structure of Bothrops asper myotoxin II complexed with the anti-trypanosomal drug suramin Deposited 2004-12-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 2 IPA ISOPROPYL ALCOHOL × 5 SVR 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；PEG 3350, isopropanol, sodium citrate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.240

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PA22_BOTAS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–121； UniProt 1–121 Author chain B； PDBConstruct 1–121； UniProt 1–121

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	1clp
Deposition date deposition_date	1994-09-12
Structure title title	CRYSTAL STRUCTURE OF A CALCIUM-INDEPENDENT PHOSPHOLIPASELIKE MYOTOXIC PROTEIN FROM BOTHROPS ASPER VENOM
Keywords keywords	HYDROLASE; 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	21.96 Å
Radius of gyration Rg (electron density) rg_electron	21.47 Å
Forward intensity I(0) i0	14142300.00
Molecular weight molecular_weight	27268.0 kDa
Excluded volume excluded_volume	33748 Å³
Envelope volume envelope_volume	40133 Å³
Hydration-shell volume shell_volume	16627 Å³
Envelope diameter envelope_diameter	77.8 Å
Shell Rg shell_rg	26.65 Å
Envelope Rg envelope_rg	21.62 Å
Shape Rg shape_rg	21.42 Å
Total Rg total_rg	22.33 Å
Total atoms total_atoms	1890
Residues n_residues	242
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	74.6 Å
Rg (real space) rg_real	22.09 Å
Rg uncertainty (real space) rg_real_error	0.65 Å
I(0) (real space) i0_real	1.4140e+07
I(0) uncertainty (real space) i0_real_error	1.8980e+05
Rg (reciprocal space) rg_reciprocal	22.07 Å
I(0) (reciprocal space) i0_reciprocal	14140000.0000
Solution quality estimate total_estimate	0.7875
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.3 Å
Skewness Skewness skewness	0.401
Kurtosis Kurtosis kurtosis	-0.471
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1795000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.835; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.731; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1clpa_
Class class	a — All alpha proteins
Fold Fold fold	a.133 — Phospholipase A2, PLA2
Superfamily Superfamily superfamily	a.133.1 — Phospholipase A2, PLA2
Family Family family	a.133.1.2 — Vertebrate phospholipase A2

Domain ID domain_id	d1clpb_
Class class	a — All alpha proteins
Fold Fold fold	a.133 — Phospholipase A2, PLA2
Superfamily Superfamily superfamily	a.133.1 — Phospholipase A2, PLA2
Family Family family	a.133.1.2 — Vertebrate phospholipase A2

CATH v4.4 (2 domains)

Domain ID domain_id	1clpA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	90 — Phospholipase A2
Homologous superfamily homologous superfamily	10 — Phospholipase A2 domain

Domain ID domain_id	1clpB00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	90 — Phospholipase A2
Homologous superfamily homologous superfamily	10 — Phospholipase A2 domain

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8. Citations (2)

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Unit-cell length a length_a	50.180 Å
Unit-cell length b length_b	67.760 Å
Unit-cell length c length_c	88.000 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	2.800 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.1650
R_work r_work	0.1650
R_free r_free	—

Description description	MYOTOXIN II
Molecular weight formula_weight	13764.1 kDa
EC 编号 ec_number	3.1.1.4
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1917

CRYSTAL STRUCTURE OF A CALCIUM-INDEPENDENT PHOSPHOLIPASELIKE MYOTOXIC PROTEIN FROM BOTHROPS ASPER VENOM

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

MYOTOXIN II

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Bothrops asper
通用名 common_name	terciopelo
NCBI Class编号 ncbi_taxonomy_id	8722

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	27

fit	/app/data/saxs_computation/cl/1clp/1clp.fit
pddf	/app/data/pr_computation/cl/1clp/1clp.pr.out
profile	/app/data/saxs_computation/cl/1clp/1clp.dat