3PMZ | pdb_00003pmz

Crystal Structure of the Complex of Acetylcholine Binding Protein and d-tubocurarine

PDB DOI: https://doi.org/10.2210/pdb3PMZ/pdb

Classification: CHOLINE-BINDING PROTEIN
Organism(s): Aplysia californica
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2010-11-18 Released: 2011-10-05
Deposition Author(s): Talley, T.T., Harel, M., Yamauchi, J.G., Radic, Z., Hansen, S., Huxford, T., Taylor, P.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free:
0.294 (Depositor), 0.288 (DCC)
R-Value Work:
0.228 (Depositor), 0.226 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The Curare Alkaloids: Analyzing the Poses of Complexes with the Acetylcholine Binding Protein in Relation to Structure and Binding Energies

Talley, T.T., Harel, M., Yamauchi, J.G., Radic, Z., Hansen, S., Huxford, T., Taylor, P.W.

To be published.

Macromolecule Content

Total Structure Weight: 259.53 kDa
Atom Count: 17,405
Modeled Residue Count: 2,119
Deposited Residue Count: 2,270
Unique protein chains: 1

Macromolecules

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| 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	227	Aplysia californica	Mutation(s): 0
UniProt
Find proteins for Q8WSF8 (Aplysia californica) Explore Q8WSF8 Go to UniProtKB: Q8WSF8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8WSF8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TUB Query on TUB Download:Ideal Coordinates CCD File SDF format, chain S [auth E] MOL2 format, chain S [auth E] mmCIF format, chain S [auth E]	S [auth E]	(1beta,1'alpha)-7',12'-dihydroxy-6,6'-dimethoxy-2,2',2'-trimethyltubocuraran-2'-ium C₃₇ H₄₁ N₂ O₆ JFJZZMVDLULRGK-VMPREFPWSA-O		Interactions Focus chain S [auth E] Interactions & Density Focus chain S [auth E]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth B] SDF format, chain N [auth B] SDF format, chain P [auth D] SDF format, chain T [auth E] SDF format, chain X [auth G] SDF format, chain Z [auth I] SDF format, chain Y [auth I] SDF format, chain W [auth F] SDF format, chain V [auth F] SDF format, chain U [auth E] SDF format, chain R [auth D] SDF format, chain Q [auth D] SDF format, chain O [auth C] SDF format, chain K [auth A] SDF format, chain AA [auth J] MOL2 format, chain L [auth A] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] MOL2 format, chain P [auth D] MOL2 format, chain T [auth E] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth I] MOL2 format, chain Y [auth I] MOL2 format, chain W [auth F] MOL2 format, chain V [auth F] MOL2 format, chain U [auth E] MOL2 format, chain R [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain O [auth C] MOL2 format, chain K [auth A] MOL2 format, chain AA [auth J] mmCIF format, chain L [auth A] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B] mmCIF format, chain P [auth D] mmCIF format, chain T [auth E] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth I] mmCIF format, chain Y [auth I] mmCIF format, chain W [auth F] mmCIF format, chain V [auth F] mmCIF format, chain U [auth E] mmCIF format, chain R [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain O [auth C] mmCIF format, chain K [auth A] mmCIF format, chain AA [auth J]	AA [auth J] K [auth A] L [auth A] M [auth B] N [auth B] AA [auth J], K [auth A], L [auth A], M [auth B], N [auth B], O [auth C], P [auth D], Q [auth D], R [auth D], T [auth E], U [auth E], V [auth F], W [auth F], X [auth G], Y [auth I], Z [auth I]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth J] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth I] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth J] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Focus chain T [auth E] Focus chain U [auth E] Focus chain V [auth F] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth I] Focus chain Z [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.44 Å
R-Value Free: 0.294 (Depositor), 0.288 (DCC)
R-Value Work: 0.228 (Depositor), 0.226 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.737	α = 90
b = 194.042	β = 90
c = 101.615	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-10-05

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-10-05
Type: Initial release
Version 1.1: 2013-07-24
Changes: Source and taxonomy
Version 1.2: 2021-03-31
Changes: Database references, Derived calculations, Source and taxonomy, Structure summary
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-11-20
Changes: Structure summary