6WBS | pdb_00006wbs

Human CFTR first nucleotide binding domain with dF508/V510D

PDB DOI: https://doi.org/10.2210/pdb6WBS/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2020-03-27 Released: 2021-04-07
Deposition Author(s): Simon, K.S., Kothe, M., Hilbert, B., Batchelor, J.D., Hurlbut, G.D.
Funding Organization(s): Cystic Fibrosis Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free:
0.213 (Depositor), 0.213 (DCC)
R-Value Work:
0.170 (Depositor), 0.172 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Determining the Molecular Mechanism of Suppressor Mutation V510D and the Contribution of Helical Unraveling to the dF508-CFTR Defect

Simon, K.S., Nagarajan, K., Mechin, I., Duffy, C., Manavalan, P., Altmann, S., Majewski, A., Foley, J., Kaczmarak, J.S., Bercury, S., Maderia, M., Hilbert, B., Batchelor, J.D., Ziegler, R., Bajko, J., Kothe, M., Scheule, R., Nair, A., Hurlbut, G.D.

To be published.

Macromolecule Content

Total Structure Weight: 51.39 kDa
Atom Count: 3,985
Modeled Residue Count: 440
Deposited Residue Count: 452
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cystic fibrosis transmembrane conductance regulator	A, B	226	Homo sapiens	Mutation(s): 1 Gene Names: CFTR, ABCC7 EC: 5.6.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P13569 (Homo sapiens) Explore P13569 Go to UniProtKB: P13569
PHAROS: P13569 GTEx: ENSG00000001626
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13569
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP Query on ATP 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]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å
R-Value Free: 0.213 (Depositor), 0.213 (DCC)
R-Value Work: 0.170 (Depositor), 0.172 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.396	α = 90
b = 81.66	β = 90
c = 100.404	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-04-07

Deposition Author(s):

Batchelor, J.D.

Funding Organization	Location	Grant Number
Cystic Fibrosis Foundation	United States	--

Revision History (Full details and data files)

Version 1.0: 2021-04-07
Type: Initial release
Version 1.1: 2023-10-18
Changes: Data collection, Database references, Refinement description

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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.