3SH1

Ac-AChBP ligand binding domain mutated to human alpha-7 nAChR

PDB DOI: https://doi.org/10.2210/pdb3SH1/pdb

Classification: RECEPTOR
Organism(s): Aplysia californica
Expression System: Homo sapiens
Mutation(s): Yes

Deposited: 2011-06-15 Released: 2011-10-26
Deposition Author(s): Nemecz, A., Taylor, P.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.258
R-Value Work: 0.213
R-Value Observed: 0.214

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 276.08 kDa
Atom Count: 18,393
Modelled Residue Count: 2,146
Deposited Residue Count: 2,300
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 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	230	Aplysia californica	Mutation(s): 25 Gene Names: LOC100533247 soluble acetylcholine receptor
UniProt
Find proteins for Q8WSF8 (Aplysia californica) Explore Q8WSF8 Go to UniProtKB: Q8WSF8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8WSF8
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K, L, M, N	2		N-Glycosylation	Interactions Focus chain K Focus chain L Focus chain M Focus chain N Interactions & Density Focus chain K Focus chain L Focus chain M Focus chain N
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O, P	3		N-Glycosylation	Interactions Focus chain O Focus chain P Interactions & Density Focus chain O Focus chain P
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MLK Query on MLK Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain FA [auth D] SDF format, chain JA [auth E] SDF format, chain MA [auth F] SDF format, chain OA [auth G] SDF format, chain R [auth A] SDF format, chain RA [auth H] SDF format, chain VA [auth I] SDF format, chain Y [auth B] SDF format, chain YA [auth J] MOL2 format, chain CA [auth C] MOL2 format, chain FA [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain MA [auth F] MOL2 format, chain OA [auth G] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth H] MOL2 format, chain VA [auth I] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth J]	CA [auth C] FA [auth D] JA [auth E] MA [auth F] OA [auth G] CA [auth C], FA [auth D], JA [auth E], MA [auth F], OA [auth G], R [auth A], RA [auth H], VA [auth I], Y [auth B], YA [auth J]	METHYLLYCACONITINE C₃₇ H₅₀ N₂ O₁₀ XLTANAWLDBYGFU-VTLKBQQISA-N		Interactions Focus chain CA [auth C] Focus chain FA [auth D] Focus chain JA [auth E] Focus chain MA [auth F] Focus chain OA [auth G] Focus chain R [auth A] Focus chain RA [auth H] Focus chain VA [auth I] Focus chain Y [auth B] Focus chain YA [auth J] Interactions & Density Focus chain CA [auth C] Focus chain FA [auth D] Focus chain JA [auth E] Focus chain MA [auth F] Focus chain OA [auth G] Focus chain R [auth A] Focus chain RA [auth H] Focus chain VA [auth I] Focus chain Y [auth B] Focus chain YA [auth J]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain IA [auth E] SDF format, chain LA [auth F] SDF format, chain TA [auth I] SDF format, chain UA [auth I] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain IA [auth E] MOL2 format, chain LA [auth F] MOL2 format, chain TA [auth I] MOL2 format, chain UA [auth I] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B]	BA [auth C] IA [auth E] LA [auth F] TA [auth I] UA [auth I] BA [auth C], IA [auth E], LA [auth F], TA [auth I], UA [auth I], W [auth B], X [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth C] Focus chain IA [auth E] Focus chain LA [auth F] Focus chain TA [auth I] Focus chain UA [auth I] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain BA [auth C] Focus chain IA [auth E] Focus chain LA [auth F] Focus chain TA [auth I] Focus chain UA [auth I] Focus chain W [auth B] Focus chain X [auth B]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain DA [auth C] SDF format, chain PA [auth G] SDF format, chain QA [auth G] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain WA [auth I] SDF format, chain XA [auth J] MOL2 format, chain DA [auth C] MOL2 format, chain PA [auth G] MOL2 format, chain QA [auth G] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain WA [auth I] MOL2 format, chain XA [auth J]	DA [auth C] PA [auth G] QA [auth G] T [auth A] U [auth A] DA [auth C], PA [auth G], QA [auth G], T [auth A], U [auth A], WA [auth I], XA [auth J]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain DA [auth C] Focus chain PA [auth G] Focus chain QA [auth G] Focus chain T [auth A] Focus chain U [auth A] Focus chain WA [auth I] Focus chain XA [auth J] Interactions & Density Focus chain DA [auth C] Focus chain PA [auth G] Focus chain QA [auth G] Focus chain T [auth A] Focus chain U [auth A] Focus chain WA [auth I] Focus chain XA [auth J]
MRD Query on MRD Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain HA [auth E] SDF format, chain KA [auth F] SDF format, chain S [auth A] SDF format, chain Z [auth B] MOL2 format, chain EA [auth D] MOL2 format, chain HA [auth E] MOL2 format, chain KA [auth F] MOL2 format, chain S [auth A] MOL2 format, chain Z [auth B]	EA [auth D], HA [auth E], KA [auth F], S [auth A], Z [auth B]	(4R)-2-METHYLPENTANE-2,4-DIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-RXMQYKEDSA-N		Interactions Focus chain EA [auth D] Focus chain HA [auth E] Focus chain KA [auth F] Focus chain S [auth A] Focus chain Z [auth B] Interactions & Density Focus chain EA [auth D] Focus chain HA [auth E] Focus chain KA [auth F] Focus chain S [auth A] Focus chain Z [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain NA [auth G] MOL2 format, chain NA [auth G]	NA [auth G]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain NA [auth G] Interactions & Density Focus chain NA [auth G]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain GA [auth E] SDF format, chain Q [auth A] SDF format, chain SA [auth I] SDF format, chain V [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain GA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain SA [auth I] MOL2 format, chain V [auth B]	AA [auth C], GA [auth E], Q [auth A], SA [auth I], V [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain GA [auth E] Focus chain Q [auth A] Focus chain SA [auth I] Focus chain V [auth B] Interactions & Density Focus chain AA [auth C] Focus chain GA [auth E] Focus chain Q [auth A] Focus chain SA [auth I] Focus chain V [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
MLK	PDBBind: 3SH1	Ki: 41 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.258
R-Value Work: 0.213
R-Value Observed: 0.214
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.793	α = 90
b = 140.183	β = 105.2
c = 136.806	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CCP4	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-10-26

Deposition Author(s):

Nemecz, A.

Taylor, P.W.

Revision History (Full details and data files)

Version 1.0: 2011-10-26
Type: Initial release
Version 1.1: 2013-07-17
Changes: Database references
Version 1.2: 2017-11-08
Changes: Advisory, Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary