5BRX | pdb_00005brx

X-ray crystal structure of Aplysia californica (Ac-AChBP) in complex with 2-pyridyl azatricyclo[3.3.1.13,7]decane; 2-pyridylazaadamantane; 2-Aza (TI-8480)

PDB DOI: https://doi.org/10.2210/pdb5BRX/pdb

Classification: ACETYLCHOLINE BINDING PROTEIN
Organism(s): Aplysia californica
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2015-06-01 Released: 2015-06-24
Deposition Author(s): Bobango, J., Sankaran, B., Park, J.F., Wu, J., Talley, T.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.235 (Depositor), 0.240 (DCC)
R-Value Work:
0.197 (Depositor), 0.200 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Comparisons of Binding Affinities for Neuronal Nicotinic Receptors (NNRs) and AChBPs

Bobango, J., Sankaran, B., Park, J.F., Wu, J., Talley, T.T.

To be published.

Macromolecule Content

Total Structure Weight: 265.33 kDa
Atom Count: 17,057
Modeled Residue Count: 2,105
Deposited Residue Count: 2,300
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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	230	Aplysia californica	Mutation(s): 1
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TI4 Query on TI4 Download Ideal Coordinates CCD File SDF format, chain W [auth F] SDF format, chain S [auth D] SDF format, chain M [auth A] SDF format, chain CA [auth I] MOL2 format, chain W [auth F] MOL2 format, chain S [auth D] MOL2 format, chain M [auth A] MOL2 format, chain CA [auth I] mmCIF format, chain W [auth F] mmCIF format, chain S [auth D] mmCIF format, chain M [auth A] mmCIF format, chain CA [auth I]	CA [auth I], M [auth A], S [auth D], W [auth F]	(2R,3S,5R,7S)-2-(pyridin-3-yl)-1-azatricyclo[3.3.1.1~3,7~]decane C₁₄ H₁₈ N₂ INDYXBQOPZTSTJ-XCCSTKFXSA-N		Interactions Focus chain CA [auth I] Focus chain M [auth A] Focus chain S [auth D] Focus chain W [auth F] Interactions & Density Focus chain CA [auth I] Focus chain M [auth A] Focus chain S [auth D] Focus chain W [auth F]
PG4 Query on PG4 Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain DA [auth J] SDF format, chain N [auth A] SDF format, chain X [auth F] SDF format, chain T [auth E] SDF format, chain Q [auth C] MOL2 format, chain AA [auth H] MOL2 format, chain DA [auth J] MOL2 format, chain N [auth A] MOL2 format, chain X [auth F] MOL2 format, chain T [auth E] MOL2 format, chain Q [auth C] mmCIF format, chain AA [auth H] mmCIF format, chain DA [auth J] mmCIF format, chain N [auth A] mmCIF format, chain X [auth F] mmCIF format, chain T [auth E] mmCIF format, chain Q [auth C]	AA [auth H] DA [auth J] N [auth A] Q [auth C] T [auth E] AA [auth H], DA [auth J], N [auth A], Q [auth C], T [auth E], X [auth F]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain DA [auth J] Focus chain N [auth A] Focus chain Q [auth C] Focus chain T [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth H] Focus chain DA [auth J] Focus chain N [auth A] Focus chain Q [auth C] Focus chain T [auth E] Focus chain X [auth F]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain Z [auth H] SDF format, chain Y [auth G] SDF format, chain V [auth F] SDF format, chain U [auth F] SDF format, chain R [auth D] SDF format, chain O [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain BA [auth I] MOL2 format, chain P [auth C] MOL2 format, chain Z [auth H] MOL2 format, chain Y [auth G] MOL2 format, chain V [auth F] MOL2 format, chain U [auth F] MOL2 format, chain R [auth D] MOL2 format, chain O [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain BA [auth I] mmCIF format, chain P [auth C] mmCIF format, chain Z [auth H] mmCIF format, chain Y [auth G] mmCIF format, chain V [auth F] mmCIF format, chain U [auth F] mmCIF format, chain R [auth D] mmCIF format, chain O [auth B] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain BA [auth I]	BA [auth I] K [auth A] L [auth A] O [auth B] P [auth C] BA [auth I], K [auth A], L [auth A], O [auth B], P [auth C], R [auth D], U [auth F], V [auth F], Y [auth G], Z [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth I] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain U [auth F] Focus chain V [auth F] Focus chain Y [auth G] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain U [auth F] Focus chain V [auth F] Focus chain Y [auth G] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.235 (Depositor), 0.240 (DCC)
R-Value Work: 0.197 (Depositor), 0.200 (DCC)
R-Value Observed: 0.198 (Depositor)

Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.297	α = 90
b = 98.297	β = 90
c = 270.242	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-06-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-06-24
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy
Version 1.2: 2024-10-16
Changes: Structure summary