2VPZ

POLYSULFIDE REDUCTASE NATIVE STRUCTURE

Structural Biology Knowledgebase: 2VPZ SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.249

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VPZ

Classification: OXIDOREDUCTASE

Total Structure Weight: 278207.00

Macromolecule Entities
Molecule Chains Length Organism Details
THIOSULFATE REDUCTASE A, E 765 Thermus thermophilus Gene Name(s): TT_C0155
NRFC PROTEIN B, F 195 Thermus thermophilus Gene Name(s): nrfC TT_C0154
HYPOTHETICAL MEMBRANE SPANNING PROTEIN C, G 253 Thermus thermophilus Gene Name(s): TT_C0153

Membrane Protein

Source: mpstruc | Group: ALPHA-HELICAL

Subgroup Name: Mo/Wbis-MGD Oxidoreductases

Protein Name: Polysulfide Reductase PsrABC (native)


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

A, E 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9- TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN- 4-ONE GUANOSINE DINUCLEOTIDE
MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE (Synonym)
C20 H26 N10 O13 P2 S2
VQAGYJCYOLHZDH-ILXWUORBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SF4
Query on SF4

A, B, E, F IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MO
Query on MO

A, E MOLYBDENUM ATOM
Mo
ZOKXTWBITQBERF-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.249
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 118.40 α = 90.00
b = 166.26 β = 90.00
c = 246.43 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-03-09
  • Released Date: 2008-06-10
  • Deposition author(s): Jormakka, M., Yokoyama, K., Yano, T., Tamakoshi, M., Akimoto, S., Shimamura, T., Curmi, P., Iwata, S.

Revision History

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