3ECR

Structure of human porphobilinogen deaminase

Structural Biology Knowledgebase: 3ECR SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.271
  • R-Value Work: 0.232

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3ECR

Classification: TRANSFERASE

Total Structure Weight: 80152.23

Macromolecule Entities
Molecule Chains Length Organism Details
Porphobilinogen deaminase A, B 364 Homo sapiens EC#: 2.5.1.61 IUBMB
Gene Name(s): HMBS Gene View PBGD UPS

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DPM
Query on DPM

A, B 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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.271
  • R-Value Work: 0.232
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 71.61 α = 90.00
b = 81.06 β = 90.00
c = 109.21 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-01
  • Released Date: 2008-09-30
  • Deposition author(s): Song, G., Li, Y., Cheng, C., Zhao, Y., Gao, A., Zhang, R., Joachimiak, A., Shaw, N., Liu, Z.J.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4