6XLC | pdb_00006xlc

Full-length Hsc82 bound to AMPPNP

PDB DOI: https://doi.org/10.2210/pdb6XLC/pdb
EM Map EMD-22239: EMDB EMDataResource

Classification: CHAPERONE
Organism(s): Saccharomyces cerevisiae S288C
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-06-28 Released: 2021-06-30
Deposition Author(s): Liu, Y.X., Sun, M., Myasnikov, A.G., Elnatan, D., Agard, D.A.
Funding Organization(s): Howard Hughes Medical Institute, American Heart Association

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.66 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 6XLC

This is version 1.1 of the entry. See complete history.

Literature

Full-length Hsc82 bound to AMPPNP

Liu, Y.X., Sun, M., Myasnikov, A.G., Elnatan, D., Agard, D.A.

To be published.

Macromolecule Content

Total Structure Weight: 163.07 kDa
Atom Count: 9,858
Modeled Residue Count: 1,212
Deposited Residue Count: 1,410
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent molecular chaperone HSC82	A, B	705	Saccharomyces cerevisiae S288C	Mutation(s): 0 Gene Names: HSC82, YMR186W, YM8010.16
UniProt
Find proteins for P15108 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P15108 Go to UniProtKB: P15108
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P15108
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP Query on ANP Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth B]	D [auth A], F [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
ANP	BindingDB: 6XLC	ΔG: min: -2.35e+1, max: 14.9 (kJ/mol) from 18 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.66 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2021-06-30

Deposition Author(s):

Myasnikov, A.G.

Funding Organization	Location	Grant Number
Howard Hughes Medical Institute	United States	--
American Heart Association	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-06-30
Type: Initial release
Version 1.1: 2024-03-06
Changes: Data collection, Database references

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.