2SKD

PYRIDOXAL PHOSPHORYLASE B IN COMPLEX WITH PHOSPHATE, GLUCOSE AND INOSINE-5'-MONOPHOSPHATE

Structural Biology Knowledgebase: 2SKD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.167

Literature

Macromolecules
Sequence Display for 2SKD

Classification: TRANSFERASE

Total Structure Weight: 98162.45

Macromolecule Entities
Molecule Chains Length Organism Details
PYRIDOXAL PHOSPHORYLASE B A 842 Oryctolagus cuniculus EC#: 2.4.1.1 IUBMB
Mutation: P609A
Details: IN COMPLEX WITH PHOSPHATE, GLUCOSE AND INOSINE-5'-MONOPHOSPHATE
Gene Name(s): PYGM Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PLP
Query on PLP

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

A ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.219
  • R-Value Work: 0.167
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 128.50 α = 90.00
b = 128.50 β = 90.00
c = 116.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1998-12-11
  • Released Date: 1998-12-16
  • Deposition author(s): Oikonomakos, N.G., Zographos, S.E., Tsitsanou, K.E., Johnson, L.N., Acharya, K.R.
  • Previous versions: 1SKD

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values