4NZB

NS9283 bound to Ls-AChBP

PDB DOI: https://doi.org/10.2210/pdb4NZB/pdb

Classification: ACETYLCHOLINE-BINDING PROTEIN
Organism(s): Lymnaea stagnalis
Mutation(s): No

Deposited: 2013-12-11 Released: 2014-07-09
Deposition Author(s): Olsen, J.A., Kastrup, J.S., Gajhede, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.240
R-Value Work: 0.207
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Macromolecule Content

Total Structure Weight: 364.64 kDa
Atom Count: 24,523
Modelled Residue Count: 2,963
Deposited Residue Count: 3,150
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 [auth G] B [auth D] C [auth E] D [auth A] E [auth B] A [auth G], B [auth D], C [auth E], D [auth A], E [auth B], F [auth C], G [auth F], H, I, J, K, L, M, N, O	210	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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NSE Query on NSE Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain DB [auth I] SDF format, chain JA [auth A] SDF format, chain JB [auth K] SDF format, chain MB [auth M] SDF format, chain QA [auth B] MOL2 format, chain CA [auth E] MOL2 format, chain DB [auth I] MOL2 format, chain JA [auth A] MOL2 format, chain JB [auth K] MOL2 format, chain MB [auth M] MOL2 format, chain QA [auth B]	CA [auth E] DB [auth I] JA [auth A] JB [auth K] MB [auth M] CA [auth E], DB [auth I], JA [auth A], JB [auth K], MB [auth M], QA [auth B]	3-[3-(pyridin-3-yl)-1,2,4-oxadiazol-5-yl]benzonitrile C₁₄ H₈ N₄ O HGFXDSQLRSWUBO-UHFFFAOYSA-N		Interactions Focus chain CA [auth E] Focus chain DB [auth I] Focus chain JA [auth A] Focus chain JB [auth K] Focus chain MB [auth M] Focus chain QA [auth B] Interactions & Density Focus chain CA [auth E] Focus chain DB [auth I] Focus chain JA [auth A] Focus chain JB [auth K] Focus chain MB [auth M] Focus chain QA [auth B]
1PE Query on 1PE Download Ideal Coordinates CCD File SDF format, chain CB [auth H] SDF format, chain DA [auth E] SDF format, chain EB [auth I] SDF format, chain KA [auth A] SDF format, chain P [auth G] SDF format, chain RA [auth B] SDF format, chain UA [auth C] SDF format, chain X [auth D] MOL2 format, chain CB [auth H] MOL2 format, chain DA [auth E] MOL2 format, chain EB [auth I] MOL2 format, chain KA [auth A] MOL2 format, chain P [auth G] MOL2 format, chain RA [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain X [auth D]	CB [auth H] DA [auth E] EB [auth I] KA [auth A] P [auth G] CB [auth H], DA [auth E], EB [auth I], KA [auth A], P [auth G], RA [auth B], UA [auth C], X [auth D]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain CB [auth H] Focus chain DA [auth E] Focus chain EB [auth I] Focus chain KA [auth A] Focus chain P [auth G] Focus chain RA [auth B] Focus chain UA [auth C] Focus chain X [auth D] Interactions & Density Focus chain CB [auth H] Focus chain DA [auth E] Focus chain EB [auth I] Focus chain KA [auth A] Focus chain P [auth G] Focus chain RA [auth B] Focus chain UA [auth C] Focus chain X [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain Q [auth G] SDF format, chain Y [auth D] MOL2 format, chain Q [auth G] MOL2 format, chain Y [auth D]	Q [auth G], Y [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain Q [auth G] Focus chain Y [auth D] Interactions & Density Focus chain Q [auth G] Focus chain Y [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain EA [auth E] SDF format, chain FA [auth E] SDF format, chain FB [auth I] SDF format, chain GA [auth E] SDF format, chain GB [auth J] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain NB [auth M] SDF format, chain R [auth G] SDF format, chain S [auth G] SDF format, chain SA [auth B] SDF format, chain T [auth G] SDF format, chain TA [auth B] SDF format, chain VA [auth C] SDF format, chain WA [auth F] SDF format, chain XA [auth F] SDF format, chain Z [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain FB [auth I] MOL2 format, chain GA [auth E] MOL2 format, chain GB [auth J] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NB [auth M] MOL2 format, chain R [auth G] MOL2 format, chain S [auth G] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth G] MOL2 format, chain TA [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth F] MOL2 format, chain XA [auth F] MOL2 format, chain Z [auth D]	BA [auth D] EA [auth E] FA [auth E] FB [auth I] GA [auth E] BA [auth D], EA [auth E], FA [auth E], FB [auth I], GA [auth E], GB [auth J], HA [auth E], IA [auth E], LA [auth A], MA [auth A], NB [auth M], R [auth G], S [auth G], SA [auth B], T [auth G], TA [auth B], VA [auth C], WA [auth F], XA [auth F], Z [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain FB [auth I] Focus chain GA [auth E] Focus chain GB [auth J] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NB [auth M] Focus chain R [auth G] Focus chain S [auth G] Focus chain SA [auth B] Focus chain T [auth G] Focus chain TA [auth B] Focus chain VA [auth C] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Z [auth D] Interactions & Density Focus chain BA [auth D] Focus chain EA [auth E] Focus chain FA [auth E] Focus chain FB [auth I] Focus chain GA [auth E] Focus chain GB [auth J] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain LA [auth A] Focus chain MA [auth A] Focus chain NB [auth M] Focus chain R [auth G] Focus chain S [auth G] Focus chain SA [auth B] Focus chain T [auth G] Focus chain TA [auth B] Focus chain VA [auth C] Focus chain WA [auth F] Focus chain XA [auth F] Focus chain Z [auth D]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain IB [auth J] MOL2 format, chain IB [auth J]	IB [auth J]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain IB [auth J] Interactions & Density Focus chain IB [auth J]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth F] SDF format, chain BB [auth F] SDF format, chain HB [auth J] SDF format, chain NA [auth A] SDF format, chain PA [auth A] SDF format, chain PB [auth O] SDF format, chain U [auth G] SDF format, chain V [auth G] SDF format, chain W [auth G] SDF format, chain YA [auth F] SDF format, chain ZA [auth F] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth F] MOL2 format, chain BB [auth F] MOL2 format, chain HB [auth J] MOL2 format, chain NA [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain PB [auth O] MOL2 format, chain U [auth G] MOL2 format, chain V [auth G] MOL2 format, chain W [auth G] MOL2 format, chain YA [auth F] MOL2 format, chain ZA [auth F]	AA [auth D] AB [auth F] BB [auth F] HB [auth J] NA [auth A] AA [auth D], AB [auth F], BB [auth F], HB [auth J], NA [auth A], PA [auth A], PB [auth O], U [auth G], V [auth G], W [auth G], YA [auth F], ZA [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain AB [auth F] Focus chain BB [auth F] Focus chain HB [auth J] Focus chain NA [auth A] Focus chain PA [auth A] Focus chain PB [auth O] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth F] Focus chain BB [auth F] Focus chain HB [auth J] Focus chain NA [auth A] Focus chain PA [auth A] Focus chain PB [auth O] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Focus chain YA [auth F] Focus chain ZA [auth F]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain KB [auth K] SDF format, chain LB [auth L] SDF format, chain OA [auth A] SDF format, chain OB [auth N] MOL2 format, chain KB [auth K] MOL2 format, chain LB [auth L] MOL2 format, chain OA [auth A] MOL2 format, chain OB [auth N]	KB [auth K], LB [auth L], OA [auth A], OB [auth N]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain KB [auth K] Focus chain LB [auth L] Focus chain OA [auth A] Focus chain OB [auth N] Interactions & Density Focus chain KB [auth K] Focus chain LB [auth L] Focus chain OA [auth A] Focus chain OB [auth N]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.240
R-Value Work: 0.207
R-Value Observed: 0.208
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 231.726	α = 90
b = 140.381	β = 89.98
c = 119.545	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-07-09

Deposition Author(s):

Olsen, J.A.

Kastrup, J.S.

Gajhede, M.

Revision History (Full details and data files)

Version 1.0: 2014-07-09
Type: Initial release
Version 1.1: 2018-05-16
Changes: Data collection
Version 1.2: 2019-12-25
Changes: Database references, Derived calculations
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.4: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary