5GNR | pdb_00005gnr

the structure of mini-MFN1 K88A in complex with GDP

• PDB DOI: https://doi.org/10.2210/pdb5GNR/pdb

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


• Deposited: 2016-07-24 Released: 2016-11-23 
• Deposition Author(s): Yan, L., Yu, C., Ming, Z., Lou, Z., Rao, Z., Hu, J.
• Funding Organization(s): National Natural Science Foundation of China, an International Early Career Scientist grant from Howard Hughes Medical Institute.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.302 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Literature

BDLP-like folding of Mitofusin 1

Qi, Y., Yan, L., Yu, C., Lou, Z., Rao, Z., Hu, J.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 47.78 kDa 
• Atom Count: 3,116 
• Modeled Residue Count: 387 
• Deposited Residue Count: 421 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitofusin-1	A	421	Homo sapiens	Mutation(s): 1  Gene Names: MFN1 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IWA4 (Homo sapiens) Explore Q8IWA4  Go to UniProtKB:  Q8IWA4
PHAROS:  Q8IWA4 GTEx:  ENSG00000171109

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	B [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.302 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.34	α = 90
b = 74.975	β = 90
c = 94.451	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data processing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-11-23 
Deposition Author(s): Yan, L., Yu, C., Ming, Z., Lou, Z., Rao, Z., Hu, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	31225006
an International Early Career Scientist grant from Howard Hughes Medical Institute.	Armenia	--

Revision History  

• Version 1.0: 2016-11-23
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Database references, Derived calculations
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Source and taxonomy
• Version 1.3: 2024-11-06
  Changes: Structure summary