3EQ1

The Crystal Structure of Human Porphobilinogen Deaminase at 2.8A resolution

Structural Biology Knowledgebase: 3EQ1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.259

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3EQ1

Classification: TRANSFERASE

Total Structure Weight: 80221.84

Macromolecule Entities
Molecule Chains Length Organism Details
Porphobilinogen deaminase A, B 361 Homo sapiens EC#: 2.5.1.61 IUBMB
Fragment: UNP residues 19-356
Mutation: R167Q
Gene Name(s): HMBS Gene View PBGD UPS

Small Molecules
Ligands 2 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
 
JSmol
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.259
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 81.08 α = 90.00
b = 104.43 β = 90.00
c = 109.73 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-09-30
  • Released Date: 2009-03-03
  • Deposition author(s): Kolstoe, S.E., Gill, R., Mohammed, F., Wood, S.P.

Revision History

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