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2crd

ANALYSIS OF SIDE-CHAIN ORGANIZATION ON A REFINED MODEL OF CHARYBDOTOXIN: STRUCTURAL AND FUNCTIONAL IMPLICATIONS

Method: SOLUTION NMR Dmax: 33.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CHARYBDOTOXIN

Leiurus quinquestriatus hebraeus

UniProt P13487

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 2–37 Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer SOLUTION NMR mmCIF provides none of the parsed experimental conditions Resolution not provided

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 2CRD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BAH A TWO DISULFIDE DERIVATIVE OF CHARYBDOTOXIN WITH DISULFIDE 13-33 REPLACED BY TWO ALPHA-AMINOBUTYRIC ACIDS, NMR, 30 STRUCTURES Deposited 1996-06-06 Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–37（36 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；278 K
Resolution not provided
1CMR NMR SOLUTION STRUCTURE OF A CHIMERIC PROTEIN, DESIGNED BY TRANSFERRING A FUNCTIONAL SNAKE BETA-HAIRPIN INTO A SCORPION ALPHA/BETA SCAFFOLD (PH 3.5, 20C), NMR, 18 STRUCTURES Deposited 1996-03-15 Different construct Different mutation/modification Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 7–37（31 aa）
Mutation：R19K, K21W, M23D, N24H, K25R, K26G, R28I, Y30E No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3.5；293 K
Resolution not provided
4JTA Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Charybdotoxin Deposited 2013-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain Y 23–59（37 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 K POTASSIUM ION × 12 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；293 K；PEG 400, POTASSIUM CHLORIDE, TRIS , pH 8.9, vapor diffusion, hanging drop, temperature 293K
Resolution 2.50 Å R-free 0.236
4JTC Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Charybdotoxin in Cs+ Deposited 2013-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain Y 23–59（37 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 CS CESIUM ION × 16 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；293 K；PEG 400, Cesium CHLORIDE, TRIS BUFFER, pH 8.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.56 Å R-free 0.262
4JTD Crystal structure of Kv1.2-2.1 paddle chimera channel in complex with Lys27Met mutant of Charybdotoxin Deposited 2013-03-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 9 PDB declaration: nonameric
Chain Y 23–59（37 aa） Fragment：Charybdotoxin
Mutation：K27M Non-standard monomer：Yes (specific site not provided by mmCIF) NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 4 K POTASSIUM ION × 16 PGW (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.9；293 K；PEG 400, POTASSIUM CHLORIDE, TRIS , pH 8.9, vapor diffusion, hanging drop, temperature 293K
Resolution 2.54 Å R-free 0.235

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SCKA_LEIQH
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–37； UniProt 2–37

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

SAXS profile for 2crd

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2crd
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2crd
Deposition date deposition_date1993-02-17
Structure title titleANALYSIS OF SIDE-CHAIN ORGANIZATION ON A REFINED MODEL OF CHARYBDOTOXIN: STRUCTURAL AND FUNCTIONAL IMPLICATIONS
Keywords keywordsNEUROTOXIN; NEUROTOXIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier8.77 Å
Radius of gyration Rg (electron density) rg_electron9.02 Å
Forward intensity I(0) i050074600.00
Molecular weight molecular_weight51696.0 kDa
Excluded volume excluded_volume61961 ų
Envelope volume envelope_volume8518 ų
Hydration-shell volume shell_volume7389 ų
Envelope diameter envelope_diameter32.8 Å
Shell Rg shell_rg15.43 Å
Envelope Rg envelope_rg10.47 Å
Shape Rg shape_rg9.03 Å
Total Rg total_rg9.27 Å
Total atoms total_atoms6924
Residues n_residues432
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax33.4 Å
Rg (real space) rg_real8.75 Å
Rg uncertainty (real space) rg_real_error0.43 Å
I(0) (real space) i0_real5.0070e+07
I(0) uncertainty (real space) i0_real_error5.3010e+05
Rg (reciprocal space) rg_reciprocal8.75 Å
I(0) (reciprocal space) i0_reciprocal50070000.0000
Solution quality estimate total_estimate0.8177
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary10.6 Å
Skewness Skewness skewness0.293
Kurtosis Kurtosis kurtosis-0.213
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha33990.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.600; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.830; Smooth: 0.998
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2crda_
Class classg — Small proteins
Fold Fold foldg.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamilyg.3.7 — Scorpion toxin-like
Family Family familyg.3.7.2 — Short-chain scorpion toxins
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8. Citations (2)

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9. Files and Curves (10)