4FRR

X-ray structure of Acetylcholine binding protein from Aplysia californica in presence of 3-((S)-azetidin-2-ylmethoxy)-5-((1S,2R)-2-(2-methoxyethyl)cyclopropyl)pyridine

PDB DOI: https://doi.org/10.2210/pdb4FRR/pdb

Classification: ACETYLCHOLINE BINDING PROTEIN
Organism(s): Aplysia californica
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2012-06-26 Released: 2013-10-16
Deposition Author(s): Mukhopadhyay, S., Mesecar, A.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.246
R-Value Work: 0.197
R-Value Observed: 0.200

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

X-ray structure of Acetylcholine binding protein from Aplysia californica in presence of 3-((S)-azetidin-2-ylmethoxy)-5-((1S,2R)-2-(2-methoxyethyl)cyclopropyl)pyridine

Mukhopadhyay, S., Mesecar, A.D.

To be published.

Macromolecule Content

Total Structure Weight: 265.19 kDa
Atom Count: 18,186
Modelled Residue Count: 2,102
Deposited Residue Count: 2,320
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble acetylcholine receptor	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	232	Aplysia californica	Mutation(s): 0
UniProt
Find proteins for Q8WSF8 (Aplysia californica) Explore Q8WSF8 Go to UniProtKB: Q8WSF8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8WSF8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0VC Query on 0VC Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain Y [auth E] SDF format, chain CA [auth F] SDF format, chain IA [auth H] SDF format, chain NA [auth J] SDF format, chain T [auth C] MOL2 format, chain K [auth A] MOL2 format, chain Y [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain IA [auth H] MOL2 format, chain NA [auth J] MOL2 format, chain T [auth C] mmCIF format, chain K [auth A] mmCIF format, chain Y [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain IA [auth H] mmCIF format, chain NA [auth J] mmCIF format, chain T [auth C]	CA [auth F] IA [auth H] K [auth A] NA [auth J] T [auth C] CA [auth F], IA [auth H], K [auth A], NA [auth J], T [auth C], Y [auth E]	3-[(2S)-azetidin-2-ylmethoxy]-5-[(1S,2R)-2-(2-methoxyethyl)cyclopropyl]pyridine C₁₅ H₂₂ N₂ O₂ NMIIKXFGCKOYRV-WHOFXGATSA-N		Interactions Focus chain CA [auth F] Focus chain IA [auth H] Focus chain K [auth A] Focus chain NA [auth J] Focus chain T [auth C] Focus chain Y [auth E] Interactions & Density Focus chain CA [auth F] Focus chain IA [auth H] Focus chain K [auth A] Focus chain NA [auth J] Focus chain T [auth C] Focus chain Y [auth E]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain KA [auth I] SDF format, chain LA [auth I] SDF format, chain MA [auth I] SDF format, chain OA [auth J] SDF format, chain U [auth C] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth E] SDF format, chain AA [auth E] SDF format, chain BA [auth E] SDF format, chain DA [auth F] SDF format, chain EA [auth F] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain HA [auth G] SDF format, chain JA [auth H] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth J] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain V [auth C] MOL2 format, chain KA [auth I] MOL2 format, chain LA [auth I] MOL2 format, chain MA [auth I] MOL2 format, chain OA [auth J] MOL2 format, chain U [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain JA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain V [auth C] mmCIF format, chain KA [auth I] mmCIF format, chain LA [auth I] mmCIF format, chain MA [auth I] mmCIF format, chain OA [auth J] mmCIF format, chain U [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain JA [auth H] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth J] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain V [auth C]	AA [auth E] BA [auth E] DA [auth F] EA [auth F] FA [auth G] AA [auth E], BA [auth E], DA [auth F], EA [auth F], FA [auth G], GA [auth G], HA [auth G], JA [auth H], KA [auth I], L [auth A], LA [auth I], M [auth A], MA [auth I], N [auth A], O [auth A], OA [auth J], P [auth A], PA [auth J], Q [auth B], R [auth B], S [auth B], U [auth C], V [auth C], W [auth D], X [auth D], Z [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain KA [auth I] Focus chain L [auth A] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth J] Focus chain P [auth A] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain DA [auth F] Focus chain EA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain HA [auth G] Focus chain JA [auth H] Focus chain KA [auth I] Focus chain L [auth A] Focus chain LA [auth I] Focus chain M [auth A] Focus chain MA [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth J] Focus chain P [auth A] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.246
R-Value Work: 0.197
R-Value Observed: 0.200
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.27	α = 90
b = 139.735	β = 90
c = 146.399	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
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: 2013-10-16

Deposition Author(s):

Mukhopadhyay, S.

Mesecar, A.D.

Revision History (Full details and data files)

Version 1.0: 2013-10-16
Type: Initial release
Version 1.1: 2017-11-15
Changes: Refinement description
Version 1.2: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-11-20
Changes: Structure summary