5TVH | pdb_00005tvh

Crystal structure of AChBP from Aplysia californica complex with 2-aminopyrimidine at pH 8.0 spacegroup P21

PDB DOI: https://doi.org/10.2210/pdb5TVH/pdb

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

Deposited: 2016-11-08 Released: 2017-11-15
Deposition Author(s): Camacho-Hernandez, G.A., Kaczanowska, K., Harel, M., Finn, M.G., Taylor, P.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.247 (Depositor), 0.251 (DCC)
R-Value Work:
0.191 (Depositor), 0.196 (DCC)
R-Value Observed:
0.193 (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

Crystal structure of AChBP from Aplysia californica complex with 2-aminopyrimidine at pH 7.0 spacegroup P212121

Camacho-Hernandez, G.A., Kaczanowska, K., Harel, M., Finn, M.G., Taylor, P.W.

To be published.

Macromolecule Content

Total Structure Weight: 133.23 kDa
Atom Count: 8,821
Modeled Residue Count: 1,064
Deposited Residue Count: 1,150
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	230	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
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain D
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7KO Query on 7KO Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain N [auth E] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain K [auth C] MOL2 format, chain N [auth E] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain K [auth C] mmCIF format, chain N [auth E] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], K [auth C], N [auth E]	6-chloro-N~4~,N~4~-bis[(pyridin-3-yl)methyl]pyrimidine-2,4-diamine C₁₆ H₁₅ Cl N₆ JDMRUOFJLDXEIQ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth E] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth E]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain L [auth D] MOL2 format, chain L [auth D] mmCIF format, chain L [auth D]	L [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain L [auth D] Interactions & Density Focus chain L [auth D]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain M [auth D] mmCIF format, chain O [auth E] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A], I [auth B], M [auth D], O [auth E]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain M [auth D] Focus chain O [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain M [auth D] Focus chain O [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free: 0.247 (Depositor), 0.251 (DCC)
R-Value Work: 0.191 (Depositor), 0.196 (DCC)
R-Value Observed: 0.193 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.78	α = 90
b = 88.1	β = 97.5
c = 115.5	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-11-15

Deposition Author(s):

Camacho-Hernandez, G.A.

Revision History (Full details and data files)

Version 1.0: 2017-11-15
Type: Initial release
Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.2: 2021-03-24
Changes: Source and taxonomy, Structure summary
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.4: 2024-10-23
Changes: Structure summary

5TVH | pdb_00005tvh

Crystal structure of AChBP from Aplysia californica complex with 2-aminopyrimidine at pH 8.0 spacegroup P21

Literature

Crystal structure of AChBP from Aplysia californica complex with 2-aminopyrimidine at pH 7.0 spacegroup P212121

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

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