2FP4

Crystal structure of pig GTP-specific succinyl-CoA synthetase in complex with GTP

  • Classification: LIGASE
  • Deposited: 2006-01-15 Released: 2006-02-21
  • Deposition author(s): Fraser, M.E.
  • Organism: Sus scrofa
  • Expression System: Escherichia coli BL21(DE3), Escherichia coli BL21(DE3)
  • Mutation(s): 1

Structural Biology Knowledgebase: 2FP4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2FP4

Classification: LIGASE

Total Structure Weight: 75915.02

Macromolecule Entities
Molecule Chains Length Organism Details
Succinyl-CoA ligase [GDP-forming] alpha-chain, mitochondrial A 305 Sus scrofa EC#: 6.2.1.4 IUBMB 6.2.1.5 IUBMB
Mutation: H259X
Gene Name(s): SUCLG1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Succinyl-CoA ligase [GDP-forming] beta-chain, mitochondrial B 395 Sus scrofa EC#: 6.2.1.4 IUBMB
Gene Name(s): SUCLG2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

B GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

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

B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
NEP
Query on NEP
A L-PEPTIDE LINKING C6 H10 N3 O5 P HIS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.242
  • R-Value Work: 0.195
  • Space Group: P 65
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 132.61 α = 90.00
b = 132.61 β = 90.00
c = 72.53 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-01-15
  • Released Date: 2006-02-21
  • Deposition author(s): Fraser, M.E.

Revision History

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