2ybr

Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann

Method: X-RAY DIFFRACTION D_max: 109.2 Å Quality: EXCELLENT

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

BETA-MAMMAL TOXIN CN2

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain C； UniProt 17–82	Not recorded	SINGLE CHAIN ANTIBODY FRAGMENT 9004G × 1 SINGLE CHAIN ANTIBODY FRAGMENT 9004G × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；100 MM BIS-TRIS, PH 5.5, 25% PEG 3350 AND 200 MM (NH4)2SO4.	Resolution 2.55 Å R-free 0.247
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain F； UniProt 17–82	Not recorded	SINGLE CHAIN ANTIBODY FRAGMENT 9004G × 1 SINGLE CHAIN ANTIBODY FRAGMENT 9004G × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；100 MM BIS-TRIS, PH 5.5, 25% PEG 3350 AND 200 MM (NH4)2SO4.	Resolution 2.55 Å R-free 0.247
3	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain I； UniProt 17–82	Not recorded	SINGLE CHAIN ANTIBODY FRAGMENT 9004G × 1 SINGLE CHAIN ANTIBODY FRAGMENT 9004G × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.5；100 MM BIS-TRIS, PH 5.5, 25% PEG 3350 AND 200 MM (NH4)2SO4.	Resolution 2.55 Å R-free 0.247

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 2YBR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CN2 SOLUTION STRUCTURE OF TOXIN 2 FROM CENTRUROIDES NOXIUS HOFFMANN, A BETA SCORPION NEUROTOXIN ACTING ON SODIUM CHANNELS, NMR, 15 STRUCTURES Deposited 1998-06-21	Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 17–82（66 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 4；303 K；Pressure 1 NMR sample composition H2O/D2O	Resolution not provided
25IH Cryo-EM structure of human Nav1.6 in complex with Cn2 Deposited 2026-04-06	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 17–82（66 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 9Z9 (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en × 1 PCW 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 5 Y01 CHOLESTEROL HEMISUCCINATE × 3 CLR CHOLESTEROL × 1 P5S O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine × 1 LPE 1-O-OCTADECYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 P3X (5E,17R,20S)-23-amino-20-hydroxy-14,20-dioxo-15,19,21-trioxa-20lambda~5~-phosphatricos-5-en-17-yl hexadecanoate × 1 PT5 [(2R)-1-octadecanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phospho ryl]oxy-propan-2-yl] (8Z)-icosa-5,8,11,14-tetraenoate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
2YC1 Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann Deposited 2011-03-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 17–82（66 aa）	Not recorded	GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；1.4 M SODIUM / POTASSIUM PHOSPHATE PH 5.6	Resolution 1.90 Å R-free 0.212
2YC1 Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann Deposited 2011-03-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 17–82（66 aa）	Not recorded	GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；1.4 M SODIUM / POTASSIUM PHOSPHATE PH 5.6	Resolution 1.90 Å R-free 0.212
4V1D Ternary complex among two human derived single chain antibody fragments and Cn2 toxin from scorpion Centruroides noxius. Deposited 2014-09-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 17–82（66 aa） Fragment：UNP RESIDUES 17-82	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.1M SPG PH 8.5, 25%(W/V) PEG 1500	Resolution 3.10 Å R-free 0.229

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

View Construct and Data Evidence

UniProt name	SCX2_CENNO
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–66； UniProt 17–82 Author chain F； PDBConstruct 1–66； UniProt 17–82 Author chain I； PDBConstruct 1–66； UniProt 17–82

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	2ybr
Deposition date deposition_date	2011-03-09
Structure title title	Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann
Keywords keywords	IMMUNE SYSTEM-TOXIN COMPLEX, SCORPION TOXIN; IMMUNE SYSTEM/TOXIN
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	33.59 Å
Radius of gyration Rg (electron density) rg_electron	32.92 Å
Forward intensity I(0) i0	153793000.00
Molecular weight molecular_weight	95687.0 kDa
Excluded volume excluded_volume	118250 Å³
Envelope volume envelope_volume	157330 Å³
Hydration-shell volume shell_volume	40471 Å³
Envelope diameter envelope_diameter	119.5 Å
Shell Rg shell_rg	39.18 Å
Envelope Rg envelope_rg	32.34 Å
Shape Rg shape_rg	32.89 Å
Total Rg total_rg	33.48 Å
Total atoms total_atoms	6721
Residues n_residues	875
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	109.2 Å
Rg (real space) rg_real	33.51 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	1.5380e+08
I(0) uncertainty (real space) i0_real_error	2.3900e+06
Rg (reciprocal space) rg_reciprocal	33.57 Å
I(0) (reciprocal space) i0_reciprocal	153800000.0000
Solution quality estimate total_estimate	0.9025
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.8 Å
Skewness Skewness skewness	0.169
Kurtosis Kurtosis kurtosis	-0.571
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16360000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.961

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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	SINGLE CHAIN ANTIBODY FRAGMENT 9004G
Molecular weight formula_weight	12533.8 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D,G
Atom count atom_count	6941

EVQLVESGGGLVQPGGSLRLSCTGSGFTFDNYAMHWLRQVPGEGLEWVSGISRSSGDIDYADSVKGRFTISRDDAKKTLSLQMNSLRAEDTAVYYCARGGVGSFDTWGQGTMVTVSS

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	SINGLE CHAIN ANTIBODY FRAGMENT 9004G
Molecular weight formula_weight	15418.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

GGGGSGGGGSGGGGSEIVLTQSPATLSVSPGERATLSCRASQSVRSYLAWYQQKPGQAPRLLFSDASNRATGIPARFTGSGSGTDFTLTISSLEPEDFAIYYCQQYRYSPRTFGQGTKVEIKRAAAEQKLISEEDLNGAAHHHHHH

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 polymer

Description description	BETA-MAMMAL TOXIN CN2
Molecular weight formula_weight	7607.7 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F,I

KEGYLVDKNTGCKYECLKLGDNDYCLRECKQQYGKGAGGYCYAFACWCTHLYEQAIVWPLPNKRCS

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	220

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7. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2ybra_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2ybrb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2ybrb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2ybrc_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.7 — Scorpion toxin-like
Family Family family	g.3.7.1 — Long-chain scorpion toxins

Domain ID domain_id	d2ybrd_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2ybre1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2ybre2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2ybrf_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.7 — Scorpion toxin-like
Family Family family	g.3.7.1 — Long-chain scorpion toxins

Domain ID domain_id	d2ybrg_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2ybrh1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2ybrh2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2ybri_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.7 — Scorpion toxin-like
Family Family family	g.3.7.1 — Long-chain scorpion toxins

CATH v4.4 (9 domains)

Domain ID domain_id	2ybrA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ybrB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ybrC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	30 — Defensin A-like
Homologous superfamily homologous superfamily	10 — Knottin, scorpion toxin-like

Domain ID domain_id	2ybrD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ybrE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ybrF00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	30 — Defensin A-like
Homologous superfamily homologous superfamily	10 — Knottin, scorpion toxin-like

Domain ID domain_id	2ybrG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ybrH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2ybrI00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	30 — Defensin A-like
Homologous superfamily homologous superfamily	10 — Knottin, scorpion toxin-like

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8. Citations (1)

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Unit-cell length a length_a	69.844 Å
Unit-cell length b length_b	104.494 Å
Unit-cell length c length_c	152.550 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	12

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

Resolution resolution	2.550 Å
Low-resolution limit resolution_low	45.720 Å
R factor r_factor	0.1946
R_work r_work	0.1918
R_free r_free	0.2467

fit	/app/data/saxs_computation/yb/2ybr/2ybr.fit
pddf	/app/data/pr_computation/yb/2ybr/2ybr.pr.out
profile	/app/data/saxs_computation/yb/2ybr/2ybr.dat

Crystal structure of the human derived single chain antibody fragment (scFv) 9004G in complex with Cn2 toxin from the scorpion Centruroides noxius Hoffmann

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

BETA-MAMMAL TOXIN CN2

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 21 domains

SCOP 2.08 (12 domains)

CATH v4.4 (9 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)