3DP9

Crystal structure of Vibrio cholerae 5'-methylthioadenosine/S-adenosyl homocysteine nucleosidase (MTAN) complexed with butylthio-DADMe-Immucillin A

Structural Biology Knowledgebase: 3DP9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.200

Literature

Macromolecules
Sequence Display for 3DP9

Classification: HYDROLASE

Total Structure Weight: 49888.38

Macromolecule Entities
Molecule Chains Length Organism Details
MTA/SAH nucleosidase A, C 231 Vibrio cholerae EC#: 3.2.2.9 IUBMB
Gene Name(s): mtnN VC_2379
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, C (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin- 7-yl)methyl]-4-[(butylsulfanyl)methyl]pyrrolidin- 3-ol
butylthio-DADMe-Immucillin A (Synonym)
C16 H25 N5 O S
LTSUEVPGSXUJHT-OLZOCXBDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IOD
Query on IOD

C IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
BIG N/A in BindingDB
IC50: 6 nM  BindingMOAD
Kd: 0.208 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.264
  • R-Value Work: 0.200
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 67.74 α = 90.00
b = 54.33 β = 115.35
c = 69.79 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-07-07
  • Released Date: 2009-03-10
  • Deposition author(s): Ho, M., Gutierrez, J.A., Crowder, T., Rinaldo-Matthis, A., Almo, S.C., Schramm, V.L.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor