SAXSdb — 1vd3

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

RNase NGR3

Nicotiana glutinosa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9SSV1_NICGU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–217； UniProt 24–236

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	1vd3
Deposition date deposition_date	2004-03-18
Structure title title	Ribonuclease NT in complex with 2'-UMP
Keywords keywords	hydrolase, ribonuclease, nucleic acid, RNA; 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.

1vd3__assembly_1__model_1

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

Download this curve (.dat)

1vd3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vd3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.83 Å
Rg (electron density)	16.51 Å
Total Rg	17.56 Å
Atom count	1669
Residues	204
Excluded volume	29110 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vd3__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	RNase NGR3
Molecular weight formula_weight	24998.5 kDa
EC 编号 ec_number	3.1.27.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1764

YVEFAQDFDFFYFVQQWPASYCDTRRSCCYPTTGKPDEDFSIHGLWPNYENGKWPQNCDRESSLDESEISDLISTMEKNWPSLACPSSDGVRFWSHEWLKHGTCSALGERAYFQAALDFRKKSNLLENLKNAEITPRNGEHYTLESIKKAIEEGVGHSPYIECNVDTQGNHQIYQVYLCVDKTATDFIDCPIFPHGRGCGSKIEFPPFSSESDHDEF

Source Source

Source organism organism	Nicotiana glutinosa
NCBI taxonomy ID ncbi_taxonomy_id	35889
Host organism host_organism	Pichia pastoris

Entity 2 Entity 2 non-polymer

Description description	PHOSPHORIC ACID MONO-[2-(2,4-DIOXO-3,4-DIHYDRO-2H-PYRIMIDIN-1-YL)-4-HYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3-YL] ESTER
Molecular weight formula_weight	324.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	95

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1vd3a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.124 — Ribonuclease Rh-like
Superfamily Superfamily superfamily	d.124.1 — Ribonuclease Rh-like
Family Family family	d.124.1.1 — Ribonuclease Rh-like

CATH v4.4 (1 domains)

Domain ID domain_id	1vd3A00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	730 — Ribonuclease Rh; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease T2-like

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Unit-cell length a length_a	37.232 Å
Unit-cell length b length_b	68.984 Å
Unit-cell length c length_c	73.863 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	4

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	19.680 Å
R factor r_factor	0.2090
R_work r_work	0.2090
R_free r_free	0.2510

Ribonuclease NT in complex with 2'-UMP

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

RNase NGR3

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

1vd3__assembly_1__model_1

1vd3__assembly_1__model_1 | I(q)

1vd3__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Ribonuclease NT in complex with 2'-UMP

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

RNase NGR3

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

1vd3__assembly_1__model_1

1vd3__assembly_1__model_1 | I(q)

1vd3__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 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)