2YPN

Hydroxymethylbilane synthase

Structural Biology Knowledgebase: 2YPN SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.194

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2YPN

Classification: TRANSFERASE

Total Structure Weight: 34312.48

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (HYDROXYMETHYLBILANE SYNTHASE) A 313 Escherichia coli EC#: 2.5.1.61 IUBMB
Fragment: THREE DOMAINS
Details: CONTAINS A DIPYRROMETHANE COFACTOR LINKED TO THE RESIDUE CYSTEINE 242
Gene Name(s): hemC popE b3805 JW5932
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
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
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.269
  • R-Value Work: 0.194
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 88.06 α = 90.00
b = 75.73 β = 90.00
c = 50.35 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-01-11
  • Released Date: 1999-02-02
  • Deposition author(s): Nieh, Y.P., Raftery, J., Weisgerber, S., Habash, J., Schotte, F., Ursby, T., Wulff, M., Haedener, A., Campbell, J.W., Hao, Q., Helliwell, J.R.

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