SAXSdb — 2jdl

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

RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN

TRICHOSANTHES KIRILOWII

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	ACIDIC RIBOSOMAL PROTEIN P2 × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	ACIDIC RIBOSOMAL PROTEIN P2 × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RIPT_TRIKI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–247； UniProt 25–270 Author chain B； PDBConstruct 2–247； UniProt 25–270

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	2jdl
Deposition date deposition_date	2007-01-11
Structure title title	Structure of C-terminal region of acidic P2 ribosomal protein complexed with trichosanthin
Keywords keywords	RIBOSOME INACTIVIATING PROTEIN, RIBOSOMAL PROTEIN, PROTEIN SYNTHESIS INHIBITOR, TOXIN, HYDROLASE, PLANT DEFENSE, ANTIVIRAL PROTEIN; 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.

2jdl__assembly_1__model_1

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

Download this curve (.dat)

2jdl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2jdl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.12 Å
Rg (electron density)	17.80 Å
Total Rg	18.78 Å
Atom count	1993
Residues	257
Excluded volume	35571 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2jdl__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2jdl__assembly_2__model_1`	dimeric （2）	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	RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN
Molecular weight formula_weight	27182.9 kDa
EC 编号 ec_number	3.2.2.22
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4245

MVSFRLSGATSSSYGVFISNLRKALPNERKLYDIPLLRSSLPGSQRYALIHLTNYADETISVAIDVTNVYIMGYRAGDTSYFFNEASATEAAKYVFKDAMRKVTLPYSGNYERLQTAAGKIRENIPLGLPALDSAITTLFYYNANSAASALMVLIQSTSEAARYKFIEQQIGKRVDKTFLPSLAIISLENSWSALSKQIQIASTNNGQFESPVVLINAQNQRVTITNVDAGVVTSNIALLLNRNNMA

Source Source

Source organism organism	TRICHOSANTHES KIRILOWII
Common name common_name	MONGOLIAN SNAKE-GOURD
NCBI taxonomy ID ncbi_taxonomy_id	3677
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	ACIDIC RIBOSOMAL PROTEIN P2
Molecular weight formula_weight	1218.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

SDDDMGFGLFD

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	267

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2jdla_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamily	d.165.1 — Ribosome inactivating proteins (RIP)
Family Family family	d.165.1.1 — Plant cytotoxins

Domain ID domain_id	d2jdlb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamily	d.165.1 — Ribosome inactivating proteins (RIP)
Family Family family	d.165.1.1 — Plant cytotoxins

CATH v4.4 (4 domains)

Domain ID domain_id	2jdlA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily	10 — Ricin (A subunit), domain 1

Domain ID domain_id	2jdlA02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily	10 — Ricin (A Subunit), domain 2

Domain ID domain_id	2jdlB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily	10 — Ricin (A subunit), domain 1

Domain ID domain_id	2jdlB02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily	10 — Ricin (A Subunit), domain 2

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Unit-cell length a length_a	62.589 Å
Unit-cell length b length_b	43.964 Å
Unit-cell length c length_c	92.235 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.87 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	25.470 Å
R factor r_factor	0.1670
R_work r_work	0.1630
R_free r_free	0.2380

Structure of C-terminal region of acidic P2 ribosomal protein complexed with trichosanthin

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

RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN

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

2jdl__assembly_1__model_1

2jdl__assembly_1__model_1 | I(q)

2jdl__assembly_1__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of C-terminal region of acidic P2 ribosomal protein complexed with trichosanthin

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

RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN

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

2jdl__assembly_1__model_1

2jdl__assembly_1__model_1 | I(q)

2jdl__assembly_1__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)