4ZR6 | pdb_00004zr6

Lymnaea Stagnalis Acetylcholine Binding Protein in Complex with 3-[(4E)-4-[(3-methylimidazol-4-yl)methylene]-2,3-dihydropyrrol-5-yl]pyridine

PDB DOI: https://doi.org/10.2210/pdb4ZR6/pdb

Classification: ACETYLCHOLINE BINDING PROTEIN
Organism(s): Lymnaea stagnalis
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2015-05-11 Released: 2016-05-11
Deposition Author(s): Bobango, J., Bryant, D., Denton, T.T., Talley, T.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.266 (Depositor), 0.260 (DCC)
R-Value Work:
0.210 (Depositor)
R-Value Observed:
0.213 (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

Structure-guided design and analysis of arylidene anabaseines and myosmines

Denton, T.T., Bobango, J., Talley, T.T.

To be published.

Macromolecule Content

Total Structure Weight: 125.49 kDa
Atom Count: 7,293
Modeled Residue Count: 983
Deposited Residue Count: 1,090
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholine-binding protein	A, B, C, D, E	218	Lymnaea stagnalis	Mutation(s): 0
UniProt
Find proteins for P58154 (Lymnaea stagnalis) Explore P58154 Go to UniProtKB: P58154
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P58154
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4QW Query on 4QW Download:Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain J [auth E] SDF format, chain I [auth D] SDF format, chain G [auth B] SDF format, chain F [auth A] MOL2 format, chain H [auth C] MOL2 format, chain J [auth E] MOL2 format, chain I [auth D] MOL2 format, chain G [auth B] MOL2 format, chain F [auth A] mmCIF format, chain H [auth C] mmCIF format, chain J [auth E] mmCIF format, chain I [auth D] mmCIF format, chain G [auth B] mmCIF format, chain F [auth A]	F [auth A], G [auth B], H [auth C], I [auth D], J [auth E]	3-{(4E)-4-[(1-methyl-1H-imidazol-5-yl)methylidene]-3,4-dihydro-2H-pyrrol-5-yl}pyridine C₁₄ H₁₄ N₄ JNBFHHNJEVTWBO-YRNVUSSQSA-N		Interactions Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth B] Focus chain H [auth C] Focus chain I [auth D] Focus chain J [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.266 (Depositor), 0.260 (DCC)
R-Value Work: 0.210 (Depositor)
R-Value Observed: 0.213 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.924	α = 90
b = 78.1	β = 102.32
c = 120.502	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-05-11

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-05-11
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2024-11-06
Changes: Structure summary

4ZR6 | pdb_00004zr6

Lymnaea Stagnalis Acetylcholine Binding Protein in Complex with 3-[(4E)-4-[(3-methylimidazol-4-yl)methylene]-2,3-dihydropyrrol-5-yl]pyridine

Literature

Structure-guided design and analysis of arylidene anabaseines and myosmines

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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