SAXSdb — 3i9l

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

ADP-ribosyl cyclase

APLYSIA CALIFORNICA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	;N1-CYCLIC INOSINE 5'-DIPHOSPHORIBOSE ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NADA_APLCA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–258； UniProt 25–282 Author chain B； PDBConstruct 1–258； UniProt 25–282

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	3i9l
Deposition date deposition_date	2009-07-12
Structure title title	Crystal structure of ADP ribosyl cyclase complexed with N1-cIDPR
Keywords keywords	Homodimer, enzyme-product analog complex, ADP-ribosyl cyclase, Disulfide bond, Fertilization, Hydrolase, NAD; 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.

3i9l__assembly_1__model_1

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

Download this curve (.dat)

3i9l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3i9l__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.61 Å
Rg (electron density)	24.67 Å
Total Rg	25.63 Å
Atom count	4049
Residues	502
Excluded volume	72068 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3i9l__assembly_1__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	ADP-ribosyl cyclase
Molecular weight formula_weight	29507.9 kDa
EC 编号 ec_number	3.2.2.5
Mutation mutation	E179G
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	4664

IVPTRELENVFLGRCKDYEITRYLDILPRVRSDCSALWKDFFKAFSFKNPCDLDLGSYKDFFTSAQQQLPKNKVMFWSGVYDEAHDYANTGRKYITLEDTLPGYMLNSLVWCGQRANPGFNEKVCPDFKTCPVQARESFWGMASSSYAHSAEGEVTYMVDGSNPKVPAYRPDSFFGKYGLPNLTNKVTRVKVIVLHRLGEKIIEKCGAGSLLDLEKLVKAKHFAFDCVENPRAVLFLLCSDNPNARECRLAKRFYRIA

Source Source

Source organism organism	APLYSIA CALIFORNICA
Common name common_name	CALIFORNIA SEA HARE
NCBI taxonomy ID ncbi_taxonomy_id	6500
Host organism host_organism	Pichia Pastoris

Entity 2 Entity 2 non-polymer

Description description	;N1-CYCLIC INOSINE 5'-DIPHOSPHORIBOSE ;
Molecular weight formula_weight	542.3 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	615

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3i9la_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.14 — N-(deoxy)ribosyltransferase-like
Family Family family	c.23.14.3 — ADP ribosyl cyclase-like

Domain ID domain_id	d3i9lb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.14 — N-(deoxy)ribosyltransferase-like
Family Family family	c.23.14.3 — ADP ribosyl cyclase-like

CATH v4.4 (4 domains)

Domain ID domain_id	3i9lA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	82 — ADP Ribosyl Cyclase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — ADP Ribosyl Cyclase; Chain A, domain 1

Domain ID domain_id	3i9lA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	3i9lB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	82 — ADP Ribosyl Cyclase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — ADP Ribosyl Cyclase; Chain A, domain 1

Domain ID domain_id	3i9lB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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Unit-cell length a length_a	69.627 Å
Unit-cell length b length_b	58.303 Å
Unit-cell length c length_c	71.651 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.37 °
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	1.750 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1673
R_work r_work	0.1656
R_free r_free	0.1963

Crystal structure of ADP ribosyl cyclase complexed with N1-cIDPR

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

ADP-ribosyl cyclase

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

3i9l__assembly_1__model_1

3i9l__assembly_1__model_1 | I(q)

3i9l__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of ADP ribosyl cyclase complexed with N1-cIDPR

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

ADP-ribosyl cyclase

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

3i9l__assembly_1__model_1

3i9l__assembly_1__model_1 | I(q)

3i9l__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) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)