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3zwo

Crystal structure of ADP ribosyl cyclase complexed with reaction intermediate

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

ADP-RIBOSYL CYCLASE

APLYSIA CALIFORNICA

UniProt P29241

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein homooligomer Homooligomer Protein 2 GUANOSINE DIPHOSPHATE RIBOSE × 2 water × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 2 GUANOSINE DIPHOSPHATE RIBOSE × 2 water × 2 Consistent with protein count
3 Protein homooligomer Homooligomer Protein 2 GUANOSINE DIPHOSPHATE RIBOSE × 1 water × 2 Consistent with protein count
4 Protein homooligomer Homooligomer Protein 2 GUANOSINE DIPHOSPHATE RIBOSE × 1 ;3-(AMINOCARBONYL)-1-[(2R,3R,4S,5R)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(2-AMINO-6-OXO-1,6-DIHYDRO-9H-PURIN-9-YL)-3,4-DIHYD ROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2- YL]PYRIDINIUM ; × 1 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1lbe 1r0s 1r12 1r15 1r15 1r15 1r15 1r16 3i9j 3i9k 3i9l 3i9o

41 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex

None

View Construct and Data Evidence
UniProt name NADA_APLCA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–259； UniProt 24–282 Author chain B； PDBConstruct 1–259； UniProt 24–282 Author chain C； PDBConstruct 1–259； UniProt 24–282 Author chain D； PDBConstruct 1–259； UniProt 24–282 Author chain E； PDBConstruct 1–259； UniProt 24–282 Author chain F； PDBConstruct 1–259； UniProt 24–282 Author chain G； PDBConstruct 1–259； UniProt 24–282 Author chain H； PDBConstruct 1–259； UniProt 24–282

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_id3zwo
Deposition date deposition_date2011-08-02
Structure title titleCrystal structure of ADP ribosyl cyclase complexed with reaction intermediate
Keywords keywordsHYDROLASE, CD38, HYDROLYSIS, NAD, SUBSTRATE SPECIFICITY; HYDROLASE
Experimental Method methodX-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.

3zwo__assembly_1__model_1

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

Download this curve (.dat)

3zwo__assembly_1__model_1 | I(q)

10-2 10-1 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3zwo__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）25.64 Å
Rg (electron density)24.74 Å
Total Rg25.70 Å
Atom count4096
Residues502
Excluded volume72768 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3zwo__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3zwo__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3zwo__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3zwo__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 (4)

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd3zwoa_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.14 — N-(deoxy)ribosyltransferase-like
Family Family familyc.23.14.3 — ADP ribosyl cyclase-like
Domain ID domain_idd3zwob_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.14 — N-(deoxy)ribosyltransferase-like
Family Family familyc.23.14.3 — ADP ribosyl cyclase-like
Domain ID domain_idd3zwoc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.14 — N-(deoxy)ribosyltransferase-like
Family Family familyc.23.14.3 — ADP ribosyl cyclase-like
Domain ID domain_idd3zwod_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.14 — N-(deoxy)ribosyltransferase-like
Family Family familyc.23.14.3 — ADP ribosyl cyclase-like
Domain ID domain_idd3zwoe_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.14 — N-(deoxy)ribosyltransferase-like
Family Family familyc.23.14.3 — ADP ribosyl cyclase-like
Domain ID domain_idd3zwof_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.14 — N-(deoxy)ribosyltransferase-like
Family Family familyc.23.14.3 — ADP ribosyl cyclase-like
Domain ID domain_idd3zwog_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.14 — N-(deoxy)ribosyltransferase-like
Family Family familyc.23.14.3 — ADP ribosyl cyclase-like
Domain ID domain_idd3zwoh_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.23 — Flavodoxin-like
Superfamily Superfamily superfamilyc.23.14 — N-(deoxy)ribosyltransferase-like
Family Family familyc.23.14.3 — ADP ribosyl cyclase-like

CATH v4.4 (16 domains)

Domain ID domain_id3zwoA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology82 — ADP Ribosyl Cyclase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — ADP Ribosyl Cyclase; Chain A, domain 1
Domain ID domain_id3zwoA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3zwoB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology82 — ADP Ribosyl Cyclase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — ADP Ribosyl Cyclase; Chain A, domain 1
Domain ID domain_id3zwoB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3zwoC01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology82 — ADP Ribosyl Cyclase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — ADP Ribosyl Cyclase; Chain A, domain 1
Domain ID domain_id3zwoC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3zwoD01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology82 — ADP Ribosyl Cyclase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — ADP Ribosyl Cyclase; Chain A, domain 1
Domain ID domain_id3zwoD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3zwoE01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology82 — ADP Ribosyl Cyclase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — ADP Ribosyl Cyclase; Chain A, domain 1
Domain ID domain_id3zwoE02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3zwoF01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology82 — ADP Ribosyl Cyclase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — ADP Ribosyl Cyclase; Chain A, domain 1
Domain ID domain_id3zwoF02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3zwoG01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology82 — ADP Ribosyl Cyclase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — ADP Ribosyl Cyclase; Chain A, domain 1
Domain ID domain_id3zwoG02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id3zwoH01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology82 — ADP Ribosyl Cyclase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — ADP Ribosyl Cyclase; Chain A, domain 1
Domain ID domain_id3zwoH02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
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7. Citations (1)