3SIO

Ac-AChBP ligand binding domain (not including beta 9-10 linker) mutated to human alpha-7 nAChR

PDB DOI: https://doi.org/10.2210/pdb3SIO/pdb

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

Deposited: 2011-06-19 Released: 2011-10-26
Deposition Author(s): Nemecz, A., Taylor, P.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.230
R-Value Work: 0.182
R-Value Observed: 0.184

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: 277.71 kDa
Atom Count: 19,701
Modelled Residue Count: 2,162
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): 18 Gene Names: AChBP
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, M, O	2		N-Glycosylation	Interactions Focus chain K Focus chain M Focus chain O Interactions & Density Focus chain K Focus chain M Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	L, P	7		N-Glycosylation	Interactions Focus chain L Focus chain P Interactions & Density Focus chain L Focus chain P
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	N, Q	6		N-Glycosylation	Interactions Focus chain N Focus chain Q Interactions & Density Focus chain N Focus chain Q
Glycosylation Resources
GlyTouCan: G09724ZC GlyCosmos: G09724ZC GlyGen: G09724ZC

Small Molecules

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

Binding Affinity Annotations
ID	Source	Binding Affinity
MLK	PDBBind: 3SIO	Ki: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.32 Å
R-Value Free: 0.230
R-Value Work: 0.182
R-Value Observed: 0.184
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.218	α = 90
b = 142.366	β = 90.02
c = 144.477	γ = 90

Software Package:

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

Structure Validation

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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: 2013-06-26
Changes: Database references
Version 1.2: 2017-11-08
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2024-04-03
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

3SIO

Ac-AChBP ligand binding domain (not including beta 9-10 linker) mutated to human alpha-7 nAChR

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)