1PV8

Crystal structure of a low activity F12L mutant of human porphobilinogen synthase

Structural Biology Knowledgebase: 1PV8 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.199

Literature

Macromolecules
Sequence Display for 1PV8

Classification: lyase

Total Structure Weight: 72973.30

Macromolecule Entities
Molecule Chains Length Organism Details
Delta-aminolevulinic acid dehydratase A, B 330 Homo sapiens EC#: 4.2.1.24 IUBMB
Mutation: F12L
Gene Name(s): ALAD Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PB1
Query on PB1

A 3-(2-AMINOETHYL)-4-(AMINOMETHYL)HEPTANEDIOIC ACID
C10 H20 N2 O4
QMRGRIXXWLVLTR-HTQZYQBOSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.284
  • R-Value Work: 0.199
  • Space Group: P 63
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 89.57 α = 90.00
b = 89.57 β = 90.00
c = 153.19 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-26
  • Released Date: 2003-09-09
  • Deposition author(s): Breinig, S., Kervinen, J., Stith, L., Wasson, A.S., Fairman, R., Wlodawer, A., Zdanov, A., Jaffe, E.K.

Revision History

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