4ZJT

X-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (LsAChBP) in complex with 2-Thiophenylmethylene Anabaseine (2TAB)

PDB DOI: https://doi.org/10.2210/pdb4ZJT/pdb

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

Deposited: 2015-04-29 Released: 2015-05-13
Deposition Author(s): Bobango, J., Wu, J., Talley, T.T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.225
R-Value Work: 0.189
R-Value Observed: 0.189

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

X-ray crystal structure of Lymnaea stagnalis acetylcholine binding protein (LsAChBP) in complex with 2-Thiophenylmethylene Anabaseine (2TAB)

Bobango, J., Wu, J., Talley, T.T.

To be published.

Macromolecule Content

Total Structure Weight: 252.09 kDa
Atom Count: 17,453
Modelled Residue Count: 2,115
Deposited Residue Count: 2,180
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetylcholine-binding protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	218	Lymnaea stagnalis	Mutation(s): 0
UniProt
Find proteins for P58154 (Lymnaea stagnalis) Explore P58154 Go to UniProtKB: P58154
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P58154
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
4P6 Query on 4P6 Download Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain DA [auth J] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain T [auth E] SDF format, chain U [auth F] SDF format, chain X [auth G] SDF format, chain Y [auth H] MOL2 format, chain BA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth E] MOL2 format, chain U [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth H]	BA [auth I] DA [auth J] M [auth A] O [auth B] Q [auth C] BA [auth I], DA [auth J], M [auth A], O [auth B], Q [auth C], S [auth D], T [auth E], U [auth F], X [auth G], Y [auth H]	(3E)-3-(thiophen-2-ylmethylidene)-3,4,5,6-tetrahydro-2,3'-bipyridine C₁₅ H₁₄ N₂ S MYYXDAYQWWIEQW-ZRDIBKRKSA-N		Interactions Focus chain BA [auth I] Focus chain DA [auth J] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth F] Focus chain X [auth G] Focus chain Y [auth H] Interactions & Density Focus chain BA [auth I] Focus chain DA [auth J] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth E] Focus chain U [auth F] Focus chain X [auth G] Focus chain Y [auth H]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain CA [auth J] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain V [auth G] SDF format, chain W [auth G] SDF format, chain Z [auth I] MOL2 format, chain AA [auth I] MOL2 format, chain CA [auth J] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain V [auth G] MOL2 format, chain W [auth G] MOL2 format, chain Z [auth I]	AA [auth I] CA [auth J] K [auth A] L [auth A] N [auth B] AA [auth I], CA [auth J], K [auth A], L [auth A], N [auth B], P [auth C], R [auth D], V [auth G], W [auth G], Z [auth I]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain V [auth G] Focus chain W [auth G] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain V [auth G] Focus chain W [auth G] Focus chain Z [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.225
R-Value Work: 0.189
R-Value Observed: 0.189
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.842	α = 90
b = 127.603	β = 110.45
c = 122.469	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-05-13

Deposition Author(s):

Bobango, J.

Wu, J.

Talley, T.T.

Revision History (Full details and data files)

Version 1.0: 2015-05-13
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary