1EQB

X-RAY CRYSTAL STRUCTURE AT 2.7 ANGSTROMS RESOLUTION OF TERNARY COMPLEX BETWEEN THE Y65F MUTANT OF E-COLI SERINE HYDROXYMETHYLTRANSFERASE, GLYCINE AND 5-FORMYL TETRAHYDROFOLATE

Structural Biology Knowledgebase: 1EQB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.205

Literature

Macromolecules
Sequence Display for 1EQB

Classification: TRANSFERASE

Total Structure Weight: 184610.27

Macromolecule Entities
Molecule Chains Length Organism Details
SERINE HYDROXYMETHYLTRANSFERASE A, B, C, D 417 Escherichia coli EC#: 2.1.2.1 IUBMB
Mutation: Y65F
Gene Name(s): glyA b2551 JW2535
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8- hexahydropteridin-6-yl]methyl}amino)benzoyl]- L-glutamic acid
[6S]-5-FORMYL-TETRAHYDROFOLATE; 6S-FOLINIC ACID (Synonym)
C20 H23 N7 O7
VVIAGPKUTFNRDU-STQMWFEESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLP
Query on PLP

A, B, C, D PYRIDOXAL-5'-PHOSPHATE
VITAMIN B6 Phosphate (Synonym)
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLY
Query on GLY

A, B, C, D GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.205
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 77.74 α = 90.00
b = 172.48 β = 104.28
c = 95.41 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-04-03
  • Released Date: 2000-04-19
  • Deposition author(s): Contestabile, R., Angelaccio, S., Bossa, F., Wright, H.T., Scarsdale, N., Kazanina, G., Schirch, V.

Revision History

  • 2014-05-07
    Type: Other | Details: add MUTATION falg
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4