3M09

F98Y TMP-resistant Dihydrofolate Reductase from Staphylococcus aureus with inhibitor RAB1

Structural Biology Knowledgebase: 3M09 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.169

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3M09

Classification: Oxidoreductase / Oxidoreductase Inhibitor

Total Structure Weight: 19778.32

Macromolecule Entities
Molecule Chains Length Organism Details
Dihydrofolate reductase A 161 Staphylococcus aureus EC#: 1.5.1.3 IUBMB
Mutation: F98Y
Gene Name(s): folA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAP
Query on NAP

A NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE (Synonym)
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RAR
Query on RAR

A 5-(3,4-dimethoxy-5-{(1E)-3-oxo-3-[(1S)-1- propylphthalazin-2(1H)-yl]prop-1-en-1-yl}benzyl)pyrimidine- 2,4-diamine
(S)-3-(5-((2,4-diaminopyrimidin-5-yl)methyl)- 2,3-dimethoxyphenyl)-1-(1-propylphthalazin- 2(1H)-yl)prop-2-en-1-one (Synonym)
C27 H30 N6 O3
YGDVMSPWZQHNMB-NEQMZLFVSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
RAR IC50: 2.9 - 12.5 nM (99) BindingDB
Ki: 0.9 nM (99) BindingDB

Ki: 0.9 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.169
  • Space Group: P 61 2 2

Unit Cell:

Length (Å) Angle (°)
a = 79.18 α = 90.00
b = 79.18 β = 90.00
c = 107.88 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-03-02
  • Released Date: 2010-07-14
  • Deposition author(s): Bourne, C.R., Barrow, W.W.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4