2ddb

Crystal structure of pseudecin from Pseudechis porphyriacus

Method: X-RAY DIFFRACTION

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

Pseudecin

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 FORMIC ACID × 7 GLYCEROL × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 FORMIC ACID × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 FORMIC ACID × 8 GLYCEROL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	SODIUM ION × 1 FORMIC ACID × 4 GLYCEROL × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CRVP_PSEPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–210； UniProt 29–238 Author chain B； PDBConstruct 1–210； UniProt 29–238 Author chain C； PDBConstruct 1–210； UniProt 29–238 Author chain D； PDBConstruct 1–210； UniProt 29–238

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	2ddb
Deposition date deposition_date	2006-01-25
Structure title title	Crystal structure of pseudecin from Pseudechis porphyriacus
Keywords keywords	CRISP, snake venom, CNG channel, TOXIN; TOXIN
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.

2ddb__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ddb__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ddb__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	18.61 Å
Rg (electron density)	18.03 Å
Total Rg	19.06 Å
Atom count	1667
Residues	209
Excluded volume	29603 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ddb__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ddb__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2ddb__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2ddb__assembly_4__model_1`	monomeric （1）	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 (5)

Entity 1 Entity 1 polymer

Description description	Pseudecin
Molecular weight formula_weight	23622.3 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7362

NKKNYQKEIVDKHNALRRSVKPTARNMLQMKWNSHAAQNAKRWADRCTFAHSPPNTRTVGKLRCGENIFMSSQPFPWSGVVQAWYDEIKNFVYGIGAKPPGSVIGHYTQVVWYKSHLIGCASAKCSSSKYLYVCQYCPAGNIRGSIATPYKSGPPCADCPSACVNRLCTNPCNYNNDFSNCKSLAKKSKCQTEWIKKKCPASCFCHNKII

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	21

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	721

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d2ddba1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.111 — PR-1-like
Superfamily Superfamily superfamily	d.111.1 — PR-1-like
Family Family family	d.111.1.0 — automated matches

Domain ID domain_id	d2ddba2
Class class	g — Small proteins
Fold Fold fold	g.19 — Crisp domain-like
Superfamily Superfamily superfamily	g.19.1 — Crisp domain-like
Family Family family	g.19.1.0 — automated matches

Domain ID domain_id	d2ddbb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.111 — PR-1-like
Superfamily Superfamily superfamily	d.111.1 — PR-1-like
Family Family family	d.111.1.0 — automated matches

Domain ID domain_id	d2ddbb2
Class class	g — Small proteins
Fold Fold fold	g.19 — Crisp domain-like
Superfamily Superfamily superfamily	g.19.1 — Crisp domain-like
Family Family family	g.19.1.0 — automated matches

Domain ID domain_id	d2ddbc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.111 — PR-1-like
Superfamily Superfamily superfamily	d.111.1 — PR-1-like
Family Family family	d.111.1.0 — automated matches

Domain ID domain_id	d2ddbc2
Class class	g — Small proteins
Fold Fold fold	g.19 — Crisp domain-like
Superfamily Superfamily superfamily	g.19.1 — Crisp domain-like
Family Family family	g.19.1.0 — automated matches

Domain ID domain_id	d2ddbd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.111 — PR-1-like
Superfamily Superfamily superfamily	d.111.1 — PR-1-like
Family Family family	d.111.1.0 — automated matches

Domain ID domain_id	d2ddbd2
Class class	g — Small proteins
Fold Fold fold	g.19 — Crisp domain-like
Superfamily Superfamily superfamily	g.19.1 — Crisp domain-like
Family Family family	g.19.1.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	2ddbA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	33 — Pathogenesis-related Protein p14a
Homologous superfamily homologous superfamily	10 — CAP

Domain ID domain_id	2ddbA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	740 — Crisp domain

Domain ID domain_id	2ddbB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	33 — Pathogenesis-related Protein p14a
Homologous superfamily homologous superfamily	10 — CAP

Domain ID domain_id	2ddbB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	740 — Crisp domain

Domain ID domain_id	2ddbC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	33 — Pathogenesis-related Protein p14a
Homologous superfamily homologous superfamily	10 — CAP

Domain ID domain_id	2ddbC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	740 — Crisp domain

Domain ID domain_id	2ddbD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	33 — Pathogenesis-related Protein p14a
Homologous superfamily homologous superfamily	10 — CAP

Domain ID domain_id	2ddbD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	740 — Crisp domain

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Unit-cell length a length_a	60.707 Å
Unit-cell length b length_b	61.668 Å
Unit-cell length c length_c	251.224 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	16

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	43.270 Å
R factor r_factor	—
R_work r_work	0.2060
R_free r_free	0.2580

Crystal structure of pseudecin from Pseudechis porphyriacus

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

Pseudecin

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

2ddb__assembly_4__model_1

2ddb__assembly_4__model_1 | I(q)

2ddb__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of pseudecin from Pseudechis porphyriacus

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

Pseudecin

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

2ddb__assembly_4__model_1

2ddb__assembly_4__model_1 | I(q)

2ddb__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)