4HQP | pdb_00004hqp

Alpha7 nicotinic receptor chimera and its complex with Alpha bungarotoxin

PDB DOI: https://doi.org/10.2210/pdb4HQP/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens, Lymnaea stagnalis, Bungarus multicinctus
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2012-10-25 Released: 2013-07-17
Deposition Author(s): Li, S.X., Cheng, K., Gomoto, R., Bren, N., Huang, S., Sine, S., Chen, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.51 Å
R-Value Free:
0.321 (Depositor), 0.320 (DCC)
R-Value Work:
0.311 (Depositor), 0.311 (DCC)
R-Value Observed:
0.311 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural principles for Alpha-neurotoxin binding to and selectivity among nicotinic receptors

Li, S.X., Cheng, K., Gomoto, R., Bren, N., Huang, S., Sine, S., Chen, L.

To be published.

Macromolecule Content

Total Structure Weight: 158.46 kDa
Atom Count: 11,092
Modeled Residue Count: 1,375
Deposited Residue Count: 1,375
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha7 nicotinic receptor chimera	A, B, C, D, E	202	Homo sapiens, Lymnaea stagnalis This entity is chimeric	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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-bungarotoxin isoform V31	F, G, H, I, J	73	Bungarus multicinctus	Mutation(s): 0
UniProt
Find proteins for P60616 (Bungarus multicinctus) Explore P60616 Go to UniProtKB: P60616
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60616
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth D] SDF format, chain P [auth C] SDF format, chain O [auth C] SDF format, chain N [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth B]	L [auth A] M [auth A] N [auth B] O [auth C] P [auth C] L [auth A], M [auth A], N [auth B], O [auth C], P [auth C], Q [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.51 Å
R-Value Free: 0.321 (Depositor), 0.320 (DCC)
R-Value Work: 0.311 (Depositor), 0.311 (DCC)
R-Value Observed: 0.311 (Depositor)

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 142.15	α = 90
b = 142.15	β = 90
c = 518.135	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-07-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-07-17
Type: Initial release
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2024-11-20
Changes: Data collection, Database references, Structure summary