SAXSdb — 2vlc

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

Ribosome-inactivating protein

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 3	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 beta-D-mannopyranose × 1 beta-D-xylopyranose × 1 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 3	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 3 beta-D-mannopyranose × 1 beta-D-xylopyranose × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q94BW3_CINCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–570； UniProt 11–580 Author chain B； PDBConstruct 1–570； UniProt 11–580

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	2vlc
Deposition date deposition_date	2008-01-11
Structure title title	Crystal structure of Natural Cinnamomin (Isoform III)
Keywords keywords	RIBOSOME INHIBITING PROTEINS, TOXIN, HYDROLASE, CINNAMOMIN, PLANT DEFENSE, N-GLYCOSIDASE, PROTEIN SYNTHESIS INHIBITOR; 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.

2vlc__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2vlc__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vlc__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	26.12 Å
Rg (electron density)	25.22 Å
Total Rg	25.95 Å
Atom count	4144
Residues	518
Excluded volume	73257 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vlc__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2vlc__assembly_2__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	Ribosome-inactivating protein
Molecular weight formula_weight	63432.5 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8406

YLQLLILLPSSPFMVVEPHTLNYQTVTFTTKNATKTSYTQFIEALRAQLASGEEPHGIPVMRERSTVPDSKRFILVELSNWAADSPVTLAVDVTNAYVVAYRTGSQSFFLREDNPDPAIENLLPDTKRYTFPFSGSYTDLERVAGERREEILLGMDPLENAISALWISNLNQQRALARSLIVVIQMVAEAVRFRFIEYRVRESISRAEMFRPDPAMLSLENKWSALSNAVQQSNQGGVFSSPVELRSISNKPVYVGSVSDRVISGLAIMLFICRSTDRASSDQFIDHLLMIRPILADVADVATDADNDDTCADPEPTVRISGRNGLCVRVRDGKYNNGNPIQLWPCKQNSDVNQLWTLRRDGTIRSNGKCLTTNGYSAGDYVMIYDCRTPVTAASIWQFWANGTIINPQSALVLSAESGNPRTTLTVQADIYASRQGWLAGNNTEPFVTSIVGFNDLCMQANGDAMWVVECESSKAEQKWALYPDGSIRPHQDRDRCLTSTDNHSQGSIIIISSCSPGSEGQRWVFMNDGTILNLKNGLVMDVKGSDPSLHQIIIWPATGKPNQKWLPLL

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	beta-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	beta-D-xylopyranose
Molecular weight formula_weight	150.1 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	120

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	2vlcA01
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	2vlcA02
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	2vlcA03
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2vlcA04
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2vlcB01
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	2vlcB02
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	2vlcB03
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	2vlcB04
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	52.388 Å
Unit-cell length b length_b	126.329 Å
Unit-cell length c length_c	161.451 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	8

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

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	17.000 Å
R factor r_factor	0.2420
R_work r_work	0.2380
R_free r_free	0.3090

Crystal structure of Natural Cinnamomin (Isoform III)

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

Ribosome-inactivating protein

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

2vlc__assembly_2__model_1

2vlc__assembly_2__model_1 | I(q)

2vlc__assembly_2__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 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of Natural Cinnamomin (Isoform III)

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

Ribosome-inactivating protein

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

2vlc__assembly_2__model_1

2vlc__assembly_2__model_1 | I(q)

2vlc__assembly_2__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 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)