4ZK1 | pdb_00004zk1

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 (Depositor), 0.219 (DCC)
R-Value Work:
0.192 (Depositor), 0.194 (DCC)
R-Value Observed:
0.192 (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

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
Modeled Residue Count: 2,112
Deposited Residue Count: 2,180
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 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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] mmCIF format, chain AA [auth H] mmCIF format, chain CA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain W [auth F] mmCIF 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 Z [auth H] SDF format, chain Y [auth H] SDF format, chain V [auth F] SDF format, chain U [auth F] SDF format, chain S [auth E] SDF format, chain Q [auth D] SDF format, chain N [auth B] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain BA [auth I] MOL2 format, chain Z [auth H] MOL2 format, chain Y [auth H] MOL2 format, chain V [auth F] MOL2 format, chain U [auth F] MOL2 format, chain S [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain BA [auth I] mmCIF format, chain Z [auth H] mmCIF format, chain Y [auth H] mmCIF format, chain V [auth F] mmCIF format, chain U [auth F] mmCIF format, chain S [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain N [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] 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 (Depositor), 0.219 (DCC)
R-Value Work: 0.192 (Depositor), 0.194 (DCC)
R-Value Observed: 0.192 (Depositor)

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

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Ligand Structure Quality Assessment

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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
Version 1.2: 2024-10-23
Changes: Structure summary