2BKW

Yeast alanine:glyoxylate aminotransferase YFL030w

Structural Biology Knowledgebase: 2BKW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.199

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2BKW

Classification: TRANSFERASE

Total Structure Weight: 42604.94

Macromolecule Entities
Molecule Chains Length Organism Details
ALANINE-GLYOXYLATE AMINOTRANSFERASE 1 A 385 Saccharomyces cerevisiae EC#: 2.6.1.44 IUBMB
Details: PYRIDOXAL 5'-PHOSPHATE LINK TO A 201, GLYOXYLATE
Gene Name(s): AGX1 YFL030W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

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

A GLYOXYLIC ACID
GLYOXALATE, GLYOXYLATE (Synonym)
C2 H2 O3
HHLFWLYXYJOTON-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.57 Å
  • R-Value Free: 0.258
  • R-Value Work: 0.199
  • Space Group: P 31 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 57.40 α = 90.00
b = 57.40 β = 90.00
c = 184.50 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-02-21
  • Released Date: 2005-11-02
  • Deposition author(s): Meyer, P., Liger, D., Leulliot, N., Quevillon-Cheruel, S., Zhou, C.Z., Borel, F., Ferrer, J.L., Poupon, A., Janin, J., van Tilbeurgh, H.

Revision History

  • 2015-11-18
    Type: Function and keywords | Details: KEYWDS
  • 2015-11-18
    Type: Linkage | Details: CONECT,LINK
  • 2015-11-18
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2015-11-18
    Type: Atom nomenclature | Details: ATOM,HETATM
  • 2015-11-18
    Type: Other | Details: TER,MODRES,REMARK 525,MASTER
  • 2015-11-18
    Type: Citation | Details: JRNL
  • 2015-11-18
    Type: Entry authorship | Details: AUTHOR
  • 2015-11-18
    Type: Polymer description | Details: COMPND,SEQRES
  • 2015-11-18
    Type: Version format compliance | Details: REMARK 4
  • 2015-11-18
    Type: Geometry validation | Details: REMARK 500
  • 2015-11-18
    Type: Non-polymer description | Details: HETSYN,FORMUL,HETNAM,HET
  • 2015-11-18
    Type: Binding sites and description | Details: REMARK 800,SITE
  • 2015-11-18
    Type: Source and taxonomy | Details: SOURCE
  • 2015-11-18
    Type: Refinement description | Details: REMARK 3