3RTE

Crystal structure of tm0922, a fusion of a domain of unknown function and ADP/ATP-dependent NAD(P)H-hydrate dehydratase from Thermotoga maritima soaked with NADP and ATP.

Structural Biology Knowledgebase: 3RTE SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.162

Literature

Macromolecules
Sequence Display for 3RTE

Classification: LYASE

Total Structure Weight: 57418.62

Macromolecule Entities
Molecule Chains Length Organism Details
Putative uncharacterized protein A 502 Thermotoga maritima EC#: 4.2.1.93 IUBMB
Gene Name(s): nnr TM_0922
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Unknown peptide, probably from expression host B 7 Escherichia coli

Small Molecules
Ligands 4 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 NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ATP
Query on ATP

A ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

A POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.162
  • Space Group: I 4 2 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 122.44 α = 90.00
b = 122.44 β = 90.00
c = 155.05 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-05-03
  • Released Date: 2011-06-22
  • Deposition author(s): Shumilin, I.A., Cymborowski, M., Lesley, S.A., Minor, W.

Revision History

  • 2015-01-21
    Type: Sequence database correspondence | Details: Reference to chain B was missing
  • 2012-10-31
    Type: Citation | Details: Citation update
  • 2012-09-19
    Type: Citation | Details: Citation update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4