Powering down the Pfam website
On October 5th, we began redirecting traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will remain available at pfam-legacy.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
4534  structures 9066  species 0  interactions 532144  sequences 2246  architectures

Clan: PBP (CL0177)


Periplasmic binding protein clan Add an annotation

Periplasmic binding proteins (PBPs) consist of two large lobes that close around the bound ligand. This architecture is reiterated in transcriptional regulators, such as the lac repressors. In the process of evolution, genes encoding the PBPs have fused with genes for integral membrane proteins. Thus, diverse mammalian receptors contain extracellular ligand binding domains that are homologous to the PBPs; these include glutamate/glycine-gated ion channels such as the NMDA receptor, G protein-coupled receptors, including metabotropic glutamate, GABA-B, calcium sensing, and pheromone receptors, and atrial natriuretic peptide-guanylate cyclase receptors [2].

This clan contains 27 families and the total number of domains in the clan is 532144. The clan was built by A Bateman.

Literature references

  1. Tam R, Saier MH Jr; , Microbiol Rev 1993;57:320-346.: Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria. PUBMED:8336670 EPMC:8336670
  2. Felder CB, Graul RC, Lee AY, Merkle HP, Sadee W; , AAPS PharmSci 1999;1:E2.: The Venus flytrap of periplasmic binding proteins: an ancient protein module present in multiple drug receptors. PUBMED:11741199 EPMC:11741199


This clan contains the following 27 member families:

CypI DctP DUF3834 HisG Lig_chan-Glu_bd Lipoprotein_8 Lipoprotein_9 LysR_substrate NMT1 NMT1_2 NMT1_3 OpuAC PBP_like PBP_like_2 PDT Phosphonate-bd Porphobil_deam SBP_bac_1 SBP_bac_11 SBP_bac_3 SBP_bac_5 SBP_bac_6 SBP_bac_8 TctC Transferrin VitK2_biosynth YhfZ_C

Domain organisation

Below is a listing of the unique domain organisations or architectures from this clan. More...

Loading domain graphics...


The table below shows the number of occurrences of each domain throughout the sequence database. More...

Pfam family Num. domains Alignment
LysR_substrate (PF03466) 146371 (27.5%) View
SBP_bac_3 (PF00497) 53227 (10.0%) View
SBP_bac_5 (PF00496) 50123 (9.4%) View
SBP_bac_8 (PF13416) 44265 (8.3%) View
SBP_bac_1 (PF01547) 35190 (6.6%) View
TctC (PF03401) 26616 (5.0%) View
DctP (PF03480) 22513 (4.2%) View
NMT1 (PF09084) 21110 (4.0%) View
Lig_chan-Glu_bd (PF10613) 15390 (2.9%) View
PBP_like_2 (PF12849) 14193 (2.7%) View
SBP_bac_11 (PF13531) 13763 (2.6%) View
OpuAC (PF04069) 12352 (2.3%) View
SBP_bac_6 (PF13343) 10577 (2.0%) View
PDT (PF00800) 9771 (1.8%) View
Pfam family Num. domains Alignment
Porphobil_deam (PF01379) 9712 (1.8%) View
HisG (PF01634) 8518 (1.6%) View
NMT1_2 (PF13379) 7943 (1.5%) View
Phosphonate-bd (PF12974) 7198 (1.4%) View
NMT1_3 (PF16868) 7047 (1.3%) View
Lipoprotein_9 (PF03180) 6729 (1.3%) View
Transferrin (PF00405) 4158 (0.8%) View
VitK2_biosynth (PF02621) 2865 (0.5%) View
PBP_like (PF12727) 2107 (0.4%) View
YhfZ_C (PF14503) 237 (0.0%) View
Lipoprotein_8 (PF02030) 70 (0.0%) View
CypI (PF06646) 64 (0.0%) View
DUF3834 (PF12916) 35 (0.0%) View
Total: 27 Total: 532144 Clan alignment

Please note: Clan alignments can be very large and can cause problems for some browsers. Read the note above before viewing.

Family relationships

This diagram shows the relationships between members of this clan. More...

Species distribution

Tree controls


This tree shows the occurrence of the domains in this clan across different species. More...



For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the MSD group, to allow us to map Pfam domains onto UniProt three-dimensional structures. The table below shows the mapping between the Pfam families in this clan, the corresponding UniProt entries, and the region of the three-dimensional structures that are available for that sequence.

Loading structure mapping...