3VPD

LysX from Thermus thermophilus complexed with AMP-PNP

Structural Biology Knowledgebase: 3VPD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.196

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VPD

Classification: LIGASE

Total Structure Weight: 63028.34

Macromolecule Entities
Molecule Chains Length Organism Details
Ribosomal protein S6 modification protein A, B 281 Thermus thermophilus EC#: 6.3.2.43 IUBMB
Gene Name(s): lysX TTHA1907

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

A, B PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
Ligand Explorer
 
JSmol
BUA
Query on BUA

A, B BUTANOIC ACID
C4 H8 O2
FERIUCNNQQJTOY-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
CIT
Query on CIT

A CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.238
  • R-Value Work: 0.196
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 130.34 α = 90.00
b = 130.34 β = 90.00
c = 77.42 γ = 120.00

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