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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.283 (Depositor), 0.270 (DCC)
R-Value Work:
0.215 (Depositor), 0.210 (DCC)
R-Value Observed:
0.218 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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.

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

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ADP-RIBOSYL CYCLASE	A, B, C, D, E A, B, C, D, E, F, G, H	260	Aplysia californica	Mutation(s): 0 EC: 3.2.2.5 (PDB Primary Data), 3.2.2 (UniProt), 2.4.99.20 (UniProt)
UniProt
Find proteins for P29241 (Aplysia californica) Explore P29241 Go to UniProtKB: P29241
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P29241
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AV1 Query on AV1 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain M [auth E] SDF format, chain N [auth F] SDF format, chain O [auth G] SDF format, chain P [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain M [auth E] MOL2 format, chain N [auth F] MOL2 format, chain O [auth G] MOL2 format, chain P [auth H] mmCIF format, chain I [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth C] mmCIF format, chain M [auth E] mmCIF format, chain N [auth F] mmCIF format, chain O [auth G] mmCIF format, chain P [auth H]	I [auth A] J [auth B] K [auth C] M [auth E] N [auth F] 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		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]
CV1 Query on CV1 Download Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	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		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.283 (Depositor), 0.270 (DCC)
R-Value Work: 0.215 (Depositor), 0.210 (DCC)
R-Value Observed: 0.218 (Depositor)

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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-08-22

Deposition Author(s):

Revision History (Full details and data files)

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
Version 1.3: 2024-11-06
Changes: Structure summary