SAXSdb — 5saa

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

Uridylate-specific endoribonuclease

Severe acute respiratory syndrome coronavirus 2

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	CITRIC ACID × 6 3-[(2S)-1-(methanesulfonyl)pyrrolidin-2-yl]-5-methyl-1,2-oxazole × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	R1AB_SARS2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–349； UniProt 6453–6798 Author chain B； PDBConstruct 4–349； UniProt 6453–6798

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	5saa
Deposition date deposition_date	2021-05-19
Structure title title	PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z319891284
Keywords keywords	;SGC - Diamond I04-1 fragment screening, PanDDA, XChemExplorer, nsp15, nendoU, sars-cov-2, sars, covid, covid19, HYDROLASE-HYDROLASE inhibitor complex ;; HYDROLASE/HYDROLASE inhibitor
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.

5saa__assembly_1__model_1

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

Download this curve (.dat)

5saa__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5saa__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.31 Å
Rg (electron density)	39.66 Å
Total Rg	40.11 Å
Atom count	16662
Residues	2088
Excluded volume	298800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5saa__assembly_1__model_1`	hexameric （6）	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 (4)

Entity 1 Entity 1 polymer

Description description	Uridylate-specific endoribonuclease
Molecular weight formula_weight	39112.5 kDa
EC 编号 ec_number	3.1.-.-
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	6315

GAMSLENVAFNVVNKGHFDGQQGEVPVSIINNTVYTKVDGVDVELFENKTTLPVNVAFELWAKRNIKPVPEVKILNNLGVDIAANTVIWDYKRDAPAHISTIGVCSMTDIAKKPTETICAPLTVFFDGRVDGQVDLFRNARNGVLITEGSVKGLQPSVGPKQASLNGVTLIGEAVKTQFNYYKKVDGVVQQLPETYFTQSRNLQEFKPRSQMEIDFLELAMDEFIERYKLEGYAFEHIVYGDFSHSQLGGLHLLIGLAKRFKESPFELEDFIPMDSTVKNYFITDAQTGSSKCVCSVIDLLLDDFVEIIKSQDLSVVSKVVKVTIDYTEISFMLWCKDGHVETFYPKLQ

Source Source

Source organism organism	Severe acute respiratory syndrome coronavirus 2
Common name common_name	2019-nCoV
NCBI taxonomy ID ncbi_taxonomy_id	2697049
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	3-[(2S)-1-(methanesulfonyl)pyrrolidin-2-yl]-5-methyl-1,2-oxazole
Molecular weight formula_weight	230.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	745

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d5saaa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.48 — Nsp15 N-terminal domain-like

Domain ID domain_id	d5saaa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.294 — EndoU-like
Superfamily Superfamily superfamily	d.294.1 — EndoU-like
Family Family family	d.294.1.2 — Nsp15 C-terminal domain-like

Domain ID domain_id	d5saaa3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d5saab1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.66 — S-adenosyl-L-methionine-dependent methyltransferases
Superfamily Superfamily superfamily	c.66.1 — S-adenosyl-L-methionine-dependent methyltransferases
Family Family family	c.66.1.48 — Nsp15 N-terminal domain-like

Domain ID domain_id	d5saab2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.294 — EndoU-like
Superfamily Superfamily superfamily	d.294.1 — EndoU-like
Family Family family	d.294.1.2 — Nsp15 C-terminal domain-like

Domain ID domain_id	d5saab3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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Unit-cell length a length_a	150.176 Å
Unit-cell length b length_b	150.176 Å
Unit-cell length c length_c	111.141 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 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.239 Å
Low-resolution limit resolution_low	130.060 Å
R factor r_factor	0.1937
R_work r_work	0.1920
R_free r_free	0.2265

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z319891284

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

Uridylate-specific endoribonuclease

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

5saa__assembly_1__model_1

5saa__assembly_1__model_1 | I(q)

5saa__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (6 domains)

7. Citations (1)

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z319891284

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

Uridylate-specific endoribonuclease

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

5saa__assembly_1__model_1

5saa__assembly_1__model_1 | I(q)

5saa__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (6 domains)

7. Citations (1)