8VPH

CamA Adenine Methyltransferase Complexed to Cognate Substrate DNA and Containing Quinoline-based SGI-1027 Analog 455 and Inhibitor MC4741

• PDB DOI: https://doi.org/10.2210/pdb8VPH/pdb

• Classification: Transferase, DNA Binding Protein/DNA
• Organism(s): Clostridioides difficile
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-01-16 Released: 2024-09-25 
• Deposition Author(s): Zhou, J., Horton, J.R., Cheng, X.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.18 Å
• R-Value Free: 0.235 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

Quinoline-based compounds can inhibit diverse enzymes that act on DNA

Zhou, J., Chen, Q., Ren, R., Yang, J., Chang, C., Liu, B., Horton, J.R., Li, C., Maksoud, L., Yang, Y., Rotili, D., Jain, A.K., Zhang, X., Blumenthal, R.M., Chen, T., Gao, Y., Valente, S., Mai, A., Cheng, X.

(2024) Cell Chem Biol 

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 233.6 kDa 
• Atom Count: 15,196 
• Modelled Residue Count: 1,714 
• Deposited Residue Count: 1,815 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Site-specific DNA-methyltransferase (adenine-specific)	A, B, C	577	Clostridioides difficile	Mutation(s): 0  Gene Names:  BN1095_20232, BN1096_690041, BN1097_700039, E5F26_07025, E5F27_14470, E5F28_16275, E5F29_09620, E5F30_09400, E5F31_14185, E5F32_03810, E5F33_08870, E5F36_00990, E5F37_03060, E5F38_04245, E5F39_00835, E5F40_02785, E5F41_17405, E5F42_11180, E5F43_12285, E5F44_14865, E5F45_19095 EC: 2.1.1.72
UniProt
Find proteins for A0A031WG99 (Clostridioides difficile) Explore A0A031WG99  Go to UniProtKB:  A0A031WG99

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA Strand II	D [auth E], G, I	14	Clostridioides difficile

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA Strand I	E [auth D], F, H	14	Clostridioides difficile

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1AC7 (Subject of Investigation/LOI)	M [auth D]	N-{3-[(2-amino-6-methylpyrimidin-4-yl)amino]-5-[(dimethylamino)methyl]phenyl}-3-[(quinolin-4-yl)amino]benzamide C30 H30 N8 O FJKSIMNYGCBSRZ-UHFFFAOYSA-O
Q8Y	J [auth A], K [auth B], L [auth C]	N-(3-phenylpropyl)adenosine C19 H23 N5 O4 UBRRRMDHTZACMR-NVQRDWNXSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.18 Å
• R-Value Free: 0.235 
• R-Value Work: 0.184 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.591	α = 90
b = 161.712	β = 90
c = 235.45	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SERGUI	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-09-25 
Deposition Author(s): Zhou, J., Horton, J.R., Cheng, X.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM049245-23

Revision History  

• Version 1.0: 2024-09-25
  Type: Initial release