4ZK1

Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Protein (LsAChBP) in Complex with 3-Pyrrolylmethylene Anabaseine

PDB DOI: https://doi.org/10.2210/pdb4ZK1/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: 1.75 Å
R-Value Free: 0.216
R-Value Work: 0.192
R-Value Observed: 0.192

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Lymnaea stagnalis Acetylcholine-Binding Protein (LsAChBP) in Complex with 3-Pyrrolylmethylene Anabaseine

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

To be published.

Macromolecule Content

Total Structure Weight: 251.92 kDa
Atom Count: 17,455
Modelled Residue Count: 2,112
Deposited Residue Count: 2,180
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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
4P7 Query on 4P7 Download Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain CA [auth I] SDF format, chain DA [auth J] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain W [auth F] SDF format, chain X [auth G] MOL2 format, chain AA [auth H] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain W [auth F] MOL2 format, chain X [auth G]	AA [auth H] CA [auth I] DA [auth J] M [auth A] O [auth B] AA [auth H], CA [auth I], DA [auth J], M [auth A], O [auth B], P [auth C], R [auth D], T [auth E], W [auth F], X [auth G]	(3E)-3-(1H-pyrrol-3-ylmethylidene)-3,4,5,6-tetrahydro-2,3'-bipyridine C₁₅ H₁₅ N₃ LCDAAPCYCXHGRV-UKTHLTGXSA-N		Interactions Focus chain AA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain X [auth G] Interactions & Density Focus chain AA [auth H] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain W [auth F] Focus chain X [auth G]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain Q [auth D] SDF format, chain U [auth F] SDF format, chain BA [auth I] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain S [auth E] SDF format, chain V [auth F] SDF format, chain Y [auth H] SDF format, chain Z [auth H] MOL2 format, chain Q [auth D] MOL2 format, chain U [auth F] MOL2 format, chain BA [auth I] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain S [auth E] MOL2 format, chain V [auth F] MOL2 format, chain Y [auth H] MOL2 format, chain Z [auth H]	BA [auth I] K [auth A] L [auth A] N [auth B] Q [auth D] BA [auth I], K [auth A], L [auth A], N [auth B], Q [auth D], S [auth E], U [auth F], V [auth F], Y [auth H], Z [auth H]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain BA [auth I] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain Y [auth H] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain K [auth A] Focus chain L [auth A] Focus chain N [auth B] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain V [auth F] Focus chain Y [auth H] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.216
R-Value Work: 0.192
R-Value Observed: 0.192
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.045	α = 90
b = 127.998	β = 110.22
c = 122.6	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: 2015-05-13

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