6Z3E

Crystal structure of GDP-bound human GIMAP5, amino acid residues 1-276

• PDB DOI: https://doi.org/10.2210/pdb6Z3E/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-20 Released: 2021-12-01 
• Deposition Author(s): Schwefel, D., Daumke, O.
• Funding Organization(s): Helmholtz Association

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.268 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 

Starting Model: experimental

Literature

Crystal structure of GDP-bound human GIMAP5

Schwefel, D., Daumke, O.

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: 31.61 kDa 
• Atom Count: 1,947 
• Modelled Residue Count: 237 
• Deposited Residue Count: 278 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase IMAP family member 5	A	278	Homo sapiens	Mutation(s): 0  Gene Names: GIMAP5, IAN4L1, IAN5, IMAP3
UniProt & NIH Common Fund Data Resources
Find proteins for Q96F15 (Homo sapiens) Explore Q96F15  Go to UniProtKB:  Q96F15
PHAROS:  Q96F15 GTEx:  ENSG00000196329

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.268 
• R-Value Work: 0.215 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.28	α = 90
b = 57.23	β = 90
c = 106.76	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-12-01 
Deposition Author(s): Schwefel, D., Daumke, O.

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Funding Organization	Location	Grant Number
Helmholtz Association	Germany	--

Revision History  

• Version 1.0: 2021-12-01
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Refinement description