3C3D

Crystal structure of 2-phospho-(S)-lactate transferase from Methanosarcina mazei in complex with Fo and phosphate. Northeast Structural Genomics Consortium target MaR46

Structural Biology Knowledgebase: 3C3D SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.195

Literature

Macromolecules
Sequence Display for 3C3D

Classification: TRANSFERASE

Total Structure Weight: 141187.80

Macromolecule Entities
Molecule Chains Length Organism Details
2-phospho-L-lactate transferase A, B, C, D 311 Methanosarcina mazei EC#: 2.7.8.28 IUBMB
Gene Name(s): cofD MM_1874
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
FO1
Query on FO1

A, B, C, D 1-deoxy-1-(8-hydroxy-2,4-dioxo-3,4-dihydropyrimido[4,5- b]quinolin-10(2H)-yl)-D-ribitol
7,8-didemethyl-8-hydroxy-5-deazariboflavin (Synonym)
C16 H17 N3 O7
AUEILLWDYUBWCM-XQQFMLRXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A, B, C, D PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
FO1 N/A in BindingDB
Kd: 1380000 nM  BindingMOAD
N/A in PDBbind
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B, C, D L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.231
  • R-Value Work: 0.195
  • Space Group: P 32
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 185.28 α = 90.00
b = 185.28 β = 90.00
c = 67.79 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-01-28
  • Released Date: 2008-02-19
  • Deposition author(s): Forouhar, F., Abashidze, M., Xu, H., Grochowski, L.L., Seetharaman, J., Hussain, M., Kuzin, A.P., Chen, Y., Zhou, W., Xiao, R., Acton, T.B., Montelione, G.T., Galinier, A., White, R.H., Tong, L., Northeast Structural Genomics Consortium (NESG)

Revision History

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