2ypn Summary

pdbe.org/2ypn
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Hydroxymethylbilane synthase

The structure was published by Nieh, Y.P., Raftery, J., Weisgerber, S., et al., Campbell, J.W., Hao, Q., and Helliwell, J.R., in 1999 in a paper entitled "Accurate and highly complete synchrotron protein crystal Laue diffraction data using the ESRF CCD and the Daresbury Laue software" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.3 Å and deposited in 1999.

The experimental data on which the structure is based was also deposited.

The PDB entry contains the structure of PROTEIN (HYDROXYMETHYLBILANE SYNTHASE). This molecule has the UniProt identifier P06983 (HEM3_ECOLI)search. The sample contained 313 residues which is 100% of the natural sequence. Out of 313 residues 292 were observed and are deposited in the PDB.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule is most likely monomeric.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A PROTEIN (HYDROXYMETHYLBILANE SYNTHASE) P06983 (1-313) (HEM3_ECOLI)search Escherichia coli K-12search 100% 313 93%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P06983 (1 - 313) PROTEIN (HYDROXYMETHYLBILANE SYNTHASE) Escherichia coli

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A (P06983) Phosphate binding protein-likesearch, Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domainsearch Periplasmic binding protein-like IIsearch, Double Stranded RNA Binding Domainsearch PF01379: Porphobilinogen deaminase, dipyromethane cofactor binding domainsearch, PF03900: Porphobilinogen deaminase, C-terminal domainsearch

Chain ID Molecular function (GO) Biological process (GO) Cellular component (GO)
A (P06983) hydroxymethylbilane synthase activitysearch transferase activitysearch tetrapyrrole biosynthetic processsearch peptidyl-pyrromethane cofactor linkagesearch porphyrin-containing compound biosynthetic processsearch heme biosynthetic processsearch protoporphyrinogen IX biosynthetic processsearch cytoplasmsearch

Chain InterPro annotation
A Tetrapyrrole biosynthesis, hydroxymethylbilane synthasesearch Porphobilinogen deaminase, N-terminalsearch Porphobilinogen deaminase, C-terminalsearch Porphobilinogen deaminase, dipyrromethane cofactor binding sitesearch