2h4c

Structure of Daboiatoxin (heterodimeric PLA2 venom)

Method: X-RAY DIFFRACTION

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

Phospholipase A2-III

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Phospholipase A2-II × 1 （Q7T3T5） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Phospholipase A2-II × 1 （Q7T3T5） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Phospholipase A2-II × 1 （Q7T3T5） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Phospholipase A2-II × 1 （Q7T3T5） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	Phospholipase A2-II × 2 （Q7T3T5） water × 4	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 4	Phospholipase A2-II × 2 （Q7T3T5） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7T2R1_DABRU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–122； UniProt 17–138 Author chain C； PDBConstruct 1–122； UniProt 17–138 Author chain E； PDBConstruct 1–122； UniProt 17–138 Author chain G； PDBConstruct 1–122； UniProt 17–138

Phospholipase A2-II

OrganismNot specified

UniProt Q7T3T5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Phospholipase A2-III × 1 （Q7T2R1） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Phospholipase A2-III × 1 （Q7T2R1） water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	Phospholipase A2-III × 1 （Q7T2R1） water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	Phospholipase A2-III × 1 （Q7T2R1） water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	Phospholipase A2-III × 2 （Q7T2R1） water × 4	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 4	Phospholipase A2-III × 2 （Q7T2R1） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q7T3T5_DABRU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–122； UniProt 9–130 Author chain D； PDBConstruct 1–122； UniProt 9–130 Author chain F； PDBConstruct 1–122； UniProt 9–130 Author chain H； PDBConstruct 1–122； UniProt 9–130

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	2h4c
Deposition date deposition_date	2006-05-24
Structure title title	Structure of Daboiatoxin (heterodimeric PLA2 venom)
Keywords keywords	PHOSPHOLIPASE A2, NON-INHIBITOR ACIDIC PLA2, BASIC PLA2, HETERODIMER, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2h4c__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2h4c__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2h4c__assembly_3__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	18.52 Å
Rg (electron density)	17.43 Å
Total Rg	18.43 Å
Atom count	1920
Residues	244
Excluded volume	33645 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2h4c__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2h4c__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2h4c__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2h4c__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2h4c__assembly_5__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2h4c__assembly_6__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Phospholipase A2-III
Molecular weight formula_weight	13632.2 kDa
EC 编号 ec_number	3.1.1.4
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	7879

NFFQFAEMIVKMTGKEAVHSYAIYGCYCGWGGQGKPQDATDRCCFVHDCCYGTVNDCNPKMATYSYSFENGDIVCGDNNLCLKTVCECDRAAAICLGQNVNTYDKNYENYAISHCTEESEQC

Entity 2 Entity 2 polymer

Description description	Phospholipase A2-II
Molecular weight formula_weight	14042.0 kDa
EC 编号 ec_number	3.1.1.4
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

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

NLFQFARLIDAKQEAFSFFKYISYGCYCGWGGQGTPKDATDRCCFVHDCCYARVKGCNPKLVEYSYSYRTGKIVCGGDDPCLRAVCECDRVAAICFRENMNTYDKKYMLYSIFDCKEESDQC

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	199

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2h4ca_
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	d2h4cb_
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	d2h4cc_
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	d2h4cd_
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	d2h4ce_
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	d2h4cf_
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	d2h4cg_
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	d2h4ch_
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 (8 domains)

Domain ID domain_id	2h4cA00
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	2h4cB00
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	2h4cC00
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	2h4cD00
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	2h4cE00
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	2h4cF00
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	2h4cG00
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	2h4cH00
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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Unit-cell length a length_a	66.977 Å
Unit-cell length b length_b	66.977 Å
Unit-cell length c length_c	240.273 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.600 Å
Low-resolution limit resolution_low	7.990 Å
R factor r_factor	0.2200
R_work r_work	0.2200
R_free r_free	0.3070

Structure of Daboiatoxin (heterodimeric PLA2 venom)

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

Phospholipase A2-III

State in the Current Structure

Other States of the Same Protein in the Database

Phospholipase A2-II

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2h4c__assembly_3__model_1

2h4c__assembly_3__model_1 | I(q)

2h4c__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. 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

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Structure of Daboiatoxin (heterodimeric PLA2 venom)

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

Phospholipase A2-III

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Phospholipase A2-II

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2h4c__assembly_3__model_1

2h4c__assembly_3__model_1 | I(q)

2h4c__assembly_3__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. 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

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)