3GD7 | pdb_00003gd7

Crystal structure of human NBD2 complexed with N6-Phenylethyl-ATP (P-ATP)

• PDB DOI: https://doi.org/10.2210/pdb3GD7/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2009-02-23 Released: 2010-03-02 
• Deposition Author(s): Atwell, S., Antonysamy, S., Conners, K., Emtage, S., Gheyi, T., Lewis, H.A., Lu, F., Sauder, J.M., Wasserman, S.R., Zhao, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.308 (Depositor), 0.304 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.245 (DCC) 

Starting Model: experimental

Literature

Crystal structure of human NBD2 complexed with N6-Phenylethyl-ATP (P-ATP)

Atwell, S., Antonysamy, S., Guggino, W.B., Conners, K., Emtage, S., Gheyi, T., Hunt, J.F., Lewis, H.A., Lu, F., Sauder, J.M., Weber, P.C., Wetmore, D., Zhao, X.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 5 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 176.52 kDa 
• Atom Count: 11,834 
• Modeled Residue Count: 1,506 
• Deposited Residue Count: 1,560 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fusion complex of Cystic fibrosis transmembrane conductance regulator, residues 1193-1427 and Maltose/maltodextrin import ATP-binding protein malK, residues 219-371	A, B, C, D	390	Homo sapiens, Escherichia coli K-12 This entity is chimeric	Mutation(s): 7  Gene Names: CFTR, malK EC: 5.6.1.6 (UniProt), 7.5.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P13569 (Homo sapiens) Explore P13569  Go to UniProtKB:  P13569
PHAROS:  P13569 GTEx:  ENSG00000001626
Find proteins for P68187 (Escherichia coli (strain K12)) Explore P68187  Go to UniProtKB:  P68187
UniProt Groups	P13569P68187

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B44	E [auth A], F [auth B], G [auth C], H [auth D]	N-(2-phenylethyl)adenosine 5'-(tetrahydrogen triphosphate) C18 H24 N5 O13 P3 PSPRNONTFBJUDQ-SCFUHWHPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.308 (Depositor), 0.304 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.245 (DCC) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.837	α = 90
b = 173.725	β = 90
c = 82.574	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
d*TREK	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-02 
Deposition Author(s): Atwell, S., Antonysamy, S., Conners, K., Emtage, S., Gheyi, T., Lewis, H.A., Lu, F., Sauder, J.M., Wasserman, S.R., Zhao, X.

Revision History  

• Version 1.0: 2010-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2018-11-21
  Changes: Data collection, Structure summary
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-09-06
  Changes: Data collection, Refinement description