9DRZ | pdb_00009drz

Structure of Lichtheimia corymbifera Kinase in complex with GDP and MG

• PDB DOI: https://doi.org/10.2210/pdb9DRZ/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Lichtheimia corymbifera
• Expression System: Escherichia
• Mutation(s): No 


• Deposited: 2024-09-26 Released: 2024-10-16 
• Deposition Author(s): Wimberly-Gard, G.M., Shuman, S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.280 (Depositor), 0.283 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: in silico

Literature

Structure of Lichtheimia corymbifera Kinase in complex with GDP and MG

Wimberly-Gard, G.M., Shuman, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

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.

Macromolecule Content 

• Total Structure Weight: 58.53 kDa 
• Atom Count: 3,906 
• Modeled Residue Count: 485 
• Deposited Residue Count: 495 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
p-loop containing nucleoside triphosphatehydrolase protein	A, B, C	165	Lichtheimia corymbifera	Mutation(s): 0  Gene Names: LCOR_04030.1
UniProt
Find proteins for A0A077WSJ1 (Lichtheimia ramosa) Explore A0A077WSJ1  Go to UniProtKB:  A0A077WSJ1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP (Subject of Investigation/LOI)	D [auth A], F [auth B], H [auth C]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.280 (Depositor), 0.283 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.469	α = 90
b = 120.469	β = 90
c = 166.733	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-16 
Deposition Author(s): Wimberly-Gard, G.M., Shuman, S.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35-GM126945

Revision History  

• Version 1.0: 2024-10-16
  Type: Initial release