3VPB

ArgX from Sulfolobus tokodaii complexed with LysW/Glu/ADP/Mg/Zn/Sulfate

Structural Biology Knowledgebase: 3VPB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.187

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VPB

Classification: LIGASE

Total Structure Weight: 141740.78

Macromolecule Entities
Molecule Chains Length Organism Details
Putative acetylornithine deacetylase A, B, C, D 282 Sulfolobus tokodaii EC#: 6.3.2 IUBMB
Gene Name(s): argE argX STK_15050
Alpha-aminoadipate carrier protein lysW E, F 56 Sulfolobus tokodaii Gene Name(s): lysW STK_01925 STS023

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ADP
Query on ADP

A, B, C, D ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLU
Query on GLU

A, B, C, D GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C, D SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, E, F ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.187
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.55 α = 90.00
b = 113.99 β = 102.43
c = 78.58 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-29
  • Released Date: 2013-02-27
  • Deposition author(s): Tomita, T., Ouchi, T., Kuzuyama, T., Nishiyama, M.

Revision History

  • 2013-07-31
    Type: Citation | Details: Citation update
  • 2013-02-27
    Type: Citation | Details: Citation update