1LS3

Crystal Structure of the Complex between Rabbit Cytosolic Serine Hydroxymethyltransferase and TriGlu-5-formyl-tetrahydrofolate

Structural Biology Knowledgebase: 1LS3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.294
  • R-Value Work: 0.220

Literature

Macromolecules
Sequence Display for 1LS3

Classification: TRANSFERASE

Total Structure Weight: 214637.06

Macromolecule Entities
Molecule Chains Length Organism Details
Serine Hydroxymethyltransferase A, B, C, D 483 Oryctolagus cuniculus EC#: 2.1.2.1 IUBMB
Gene Name(s): SHMT1 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TGF
Query on TGF

B, D 2-[4-(4-{4-[(2-AMINO-5-FORMYL-4-OXO-3,4,5,6,7,8- HEXAHYDRO-PTERIDIN-6-YLMETHYL)-AMINO]-BENZOYLAMINO}- 4-CARBOXY-BUTYRYLAMINO)-4-CARBOXY-BUTYRYLAMINO]- PENTANEDIOIC ACID
TRIGLU-5-FORMYL-TETRAHYDROFOLATE (Synonym)
C30 H37 N9 O13
ZLOMJLIQXBKNHU-VJANTYMQSA-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)
GOL
Query on GOL

B, C, D GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLY
Query on GLY

A, C 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: 0.294
  • R-Value Work: 0.220
  • Space Group: P 41
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 114.08 α = 90.00
b = 114.08 β = 90.00
c = 156.72 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-05-16
  • Released Date: 2003-02-04
  • Deposition author(s): Fu, T.F., Scarsdale, J.N., Kazanina, G., Schirch, V., Wright, H.T.

Revision History

  • 2013-08-21
    Type: Non-polymer description | Details: --
  • 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