1PDA

STRUCTURE OF PORPHOBILINOGEN DEAMINASE REVEALS A FLEXIBLE MULTIDOMAIN POLYMERASE WITH A SINGLE CATALYTIC SITE

Structural Biology Knowledgebase: 1PDA SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Observed: 0.188

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1PDA

Classification: TRANSFERASE

Total Structure Weight: 34372.57

Macromolecule Entities
Molecule Chains Length Organism Details
PORPHOBILINOGEN DEAMINASE A 313 Escherichia coli EC#: 2.5.1.61 IUBMB
Mutation: G241A, A261G
Gene Name(s): hemC popE b3805 JW5932

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

A ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
DPM
Query on DPM

A 3-[5-{[3-(2-carboxyethyl)-4-(carboxymethyl)- 5-methyl-1H-pyrrol-2-yl]methyl}-4-(carboxymethyl)- 1H-pyrrol-3-yl]propanoic acid
DIPYRROMETHANE COFACTOR (Synonym)
C20 H24 N2 O8
LCAXMKQKEYTFDM-UHFFFAOYSA-N
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Observed: 0.188
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 88.00 α = 90.00
b = 75.90 β = 90.00
c = 50.50 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1992-11-17
  • Released Date: 1993-10-31
  • Deposition author(s): Louie, G.V., Brownlie, P.D., Lambert, R., Cooper, J.B., Blundell, T.L., Wood, S.P., Warren, M.J., Woodcock, S.C., Jordan, P.M.

Revision History

  • 2013-09-18
    Type: Non-polymer description | Details: Ligand DPM updated
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4