1r15

Aplysia ADP ribosyl cyclase with bound nicotinamide and R5P

Method: X-RAY DIFFRACTION

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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	;ANY 5'-MONOPHOSPHATE NUCLEOTIDE ; × 2 NICOTINAMIDE × 4	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	;ANY 5'-MONOPHOSPHATE NUCLEOTIDE ; × 2 NICOTINAMIDE × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	;ANY 5'-MONOPHOSPHATE NUCLEOTIDE ; × 2 NICOTINAMIDE × 4	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	;ANY 5'-MONOPHOSPHATE NUCLEOTIDE ; × 2 NICOTINAMIDE × 4	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 Author chain C； PDBConstruct 1–258； UniProt 25–282 Author chain D； PDBConstruct 1–258； UniProt 25–282 Author chain E； PDBConstruct 1–258； UniProt 25–282 Author chain F； PDBConstruct 1–258； UniProt 25–282 Author chain G； PDBConstruct 1–258； UniProt 25–282 Author chain H； 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	1r15
Deposition date deposition_date	2003-09-23
Structure title title	Aplysia ADP ribosyl cyclase with bound nicotinamide and R5P
Keywords keywords	ADP-ribosyl cyclase, cyclic ADP-ribose, NAADP, Ca2+ signalling, HYDROLASE; 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.

1r15__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1r15__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1r15__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	25.56 Å
Rg (electron density)	24.61 Å
Total Rg	25.57 Å
Atom count	4086
Residues	502
Excluded volume	72728 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1r15__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1r15__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1r15__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1r15__assembly_4__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	29579.9 kDa
EC 编号 ec_number	3.2.2.5
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	16344

IVPTRELENVFLGRCKDYEITRYLDILPRVRSDCSALWKDFFKAFSFKNPCDLDLGSYKDFFTSAQQQLPKNKVMFWSGVYDEAHDYANTGRKYITLEDTLPGYMLNSLVWCGQRANPGFNEKVCPDFKTCPVQARESFWGMASSSYAHSAEGEVTYMVDGSNPKVPAYRPDSFFGKYELPNLTNKVTRVKVIVLHRLGEKIIEKCGAGSLLDLEKLVKAKHFAFDCVENPRAVLFLLCSDNPNARECRLAKRFYRIA

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	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;ANY 5'-MONOPHOSPHATE NUCLEOTIDE ;
Molecular weight formula_weight	214.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	NICOTINAMIDE
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	16

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1r15a_
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	d1r15b_
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	d1r15c_
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	d1r15d_
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	d1r15e_
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	d1r15f_
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	d1r15g_
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	d1r15h_
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 (16 domains)

Domain ID domain_id	1r15A01
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	1r15A02
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	1r15B01
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	1r15B02
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	1r15C01
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	1r15C02
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	1r15D01
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	1r15D02
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	1r15E01
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	1r15E02
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	1r15F01
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	1r15F02
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	1r15G01
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	1r15G02
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	1r15H01
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	1r15H02
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	60.400 Å
Unit-cell length b length_b	75.320 Å
Unit-cell length c length_c	138.130 Å
Unit-cell angle α angle_alpha	88.16 °
Unit-cell angle β angle_beta	89.22 °
Unit-cell angle γ angle_gamma	89.09 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	33.000 Å
R factor r_factor	0.2450
R_work r_work	0.2440
R_free r_free	0.2690

Aplysia ADP ribosyl cyclase with bound nicotinamide and R5P

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

1r15__assembly_3__model_1

1r15__assembly_3__model_1 | I(q)

1r15__assembly_3__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 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Aplysia ADP ribosyl cyclase with bound nicotinamide and R5P

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

1r15__assembly_3__model_1

1r15__assembly_3__model_1 | I(q)

1r15__assembly_3__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 non-polymer

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

CATH v4.4 (16 domains)

7. Citations (1)