3ZWY

Crystal structure of ADP-ribosyl cyclase complexed with 8-bromo-ADP- ribose and cyclic 8-bromo-cyclic-ADP-ribose

• PDB DOI: https://doi.org/10.2210/pdb3ZWY/pdb

• Classification: HYDROLASE
• Organism(s): Aplysia californica
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2011-08-03 Released: 2012-08-22 
• Deposition Author(s): Kotaka, M., Graeff, R., Zhang, L.H., Lee, H.C., Hao, Q.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.283 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 

Literature

Structural Studies of Intermediates Along the Cyclization Pathway of Aplysia Adp-Ribosyl Cyclase.

Kotaka, M., Graeff, R., Chen, Z., Zhang, L.H., Lee, H.C., Hao, Q.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 242.75 kDa 
• Atom Count: 16,759 
• Modelled Residue Count: 2,011 
• Deposited Residue Count: 2,080 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-RIBOSYL CYCLASE	A, B, C, D, E, F, G, H	260	Aplysia californica	Mutation(s): 0  EC: 3.2.2.5
UniProt
Find proteins for P29241 (Aplysia californica) Explore P29241  Go to UniProtKB:  P29241

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AV1	I [auth A], J [auth B], K [auth C], M [auth E], N [auth F], O [auth G], P [auth H]	[(2R,3S,4R,5R)-5-(6-amino-8-bromo-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl [(2R,3S,4S)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate C15 H22 Br N5 O13 P2 DTBPYRLOWSYQCZ-ZVIMGNLFSA-L
CV1	L [auth D]	(2R,3R,4S,5R,13R,14S,15R,16R)-24-amino-18-bromo-3,4,14,15-tetrahydroxy-7,9,11,25,26-pentaoxa-17,19,22-triaza-1-azonia-8 ,10-diphosphapentacyclo[18.3.1.1^2,5^.1^13,16^.0^17,21^]hexacosa-1(24),18,20,22-tetraene-8,10-diolate 8,10-dioxide C15 H21 Br N5 O13 P2 WDGMEOAIDHHBSJ-AIKIOGRUSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.283 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.286	α = 87.5
b = 77.013	β = 89.27
c = 140.338	γ = 88.99

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-08-22 
Deposition Author(s): Kotaka, M., Graeff, R., Zhang, L.H., Lee, H.C., Hao, Q.

Revision History  

• Version 1.0: 2012-08-22
  Type: Initial release
  
• Version 1.1: 2012-10-31
  Changes: Other
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary