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3zwp

Crystal structure of ADP ribosyl cyclase complexed with ara-2'F-ADP- ribose at 2.1 angstrom

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 ;[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate ; × 2 water × 2 Consistent with protein count
2 Protein homooligomer Homooligomer Protein 2 ;[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate ; × 2 GLYCEROL × 2 water × 2 Consistent with protein count
3 Protein homooligomer Homooligomer Protein 2 ;[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate ; × 2 GLYCEROL × 1 water × 2 Consistent with protein count
4 Protein homooligomer Homooligomer Protein 2 ;[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3R,4R)-4-fluoro-3-hydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate ; × 2 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 3–260； UniProt 25–282 Author chain B； PDBConstruct 3–260； UniProt 25–282 Author chain C； PDBConstruct 3–260； UniProt 25–282 Author chain D； PDBConstruct 3–260； UniProt 25–282 Author chain E； PDBConstruct 3–260； UniProt 25–282 Author chain F； PDBConstruct 3–260； UniProt 25–282 Author chain G； PDBConstruct 3–260； UniProt 25–282 Author chain H； PDBConstruct 3–260； 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_id3zwp
Deposition date deposition_date2011-08-02
Structure title titleCrystal structure of ADP ribosyl cyclase complexed with ara-2'F-ADP- ribose at 2.1 angstrom
Keywords keywordsHYDROLASE, DP-RIBOSYL CYCLASE, CD38, APLYSIA, BINDING SITES, HYDROLYSIS, NAD, PROTEIN CONFORMATION, 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.

3zwp__assembly_3__model_1

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

Download this curve (.dat)

3zwp__assembly_3__model_1 | I(q)

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

3zwp__assembly_3__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）25.69 Å
Rg (electron density)24.79 Å
Total Rg25.74 Å
Atom count4105
Residues503
Excluded volume72953 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3zwp__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3zwp__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3zwp__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 3zwp__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) 26 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd3zwpa_
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_idd3zwpb1
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_idd3zwpb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3zwpc_
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_idd3zwpd_
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_idd3zwpe_
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_idd3zwpf1
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_idd3zwpf2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3zwpg_
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_idd3zwph_
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_id3zwpA01
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_id3zwpA02
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_id3zwpB01
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_id3zwpB02
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_id3zwpC01
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_id3zwpC02
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_id3zwpD01
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_id3zwpD02
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_id3zwpE01
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_id3zwpE02
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_id3zwpF01
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_id3zwpF02
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_id3zwpG01
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_id3zwpG02
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_id3zwpH01
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_id3zwpH02
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)