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77  structures 1326  species 0  interactions 3826  sequences 68  architectures

Family: E1_DerP2_DerF2 (PF02221)

Summary: ML domain

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This is the Wikipedia entry entitled "ML domain". More...

ML domain Edit Wikipedia article

ML domain
PDB 1ktj EBI.jpg
X-ray structure of Der p 2, the major house dust mite allergen
OPM superfamily91
OPM protein1nep

The MD-2-related lipid-recognition (ML) domain is implicated in lipid recognition, particularly in the recognition of pathogen related products. It has an immunoglobulin-like beta-sandwich fold similar to that of immunoglobulin E-set domains. This domain is present in the following proteins:

Human proteins containing this domain

LY86; LY96; MMD-1;


  1. ^ Lobel P, Stock AM, Friedland N, Liou HL (2003). "Structure of a cholesterol-binding protein deficient in Niemann-Pick type C2 disease". Proc. Natl. Acad. Sci. U.S.A. 100 (5): 2512–2517. doi:10.1073/pnas.0437840100. PMC 151372. PMID 12591954.
  2. ^ Kristensen O, Kastrup JS, Skov LK, Gajhede M, Larsen JN, Johannessen BR, Bolwig C, Spangfort M, Lund K (2005). "Structure of the house dust mite allergen Der f 2: implications for function and molecular basis of IgE cross-reactivity". FEBS Lett. 579 (5): 1208–12. doi:10.1016/j.febslet.2004.11.115. PMID 15710415.
This article incorporates text from the public domain Pfam and InterPro: IPR003172

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

ML domain Provide feedback

ML domain - MD-2-related lipid recognition domain. This family consists of proteins from plants, animals and fungi, including dust mite allergen Der P 2 (P49278). It has been implicate in lipid recognition, particularly in the recognition of pathogen related products. A mutation in Npc2 (Q15668) causes a rare form of Niemann-Pick type C2 disease. This domain has a similar topology to immunoglobulin domains.

Literature references

  1. Mueller GA, Benjamin DC, Rule GS; , Biochemistry 1998;37:12707-12714.: Tertiary structure of the major house dust mite allergen Der p 2: sequential and structural homologies. PUBMED:9737847 EPMC:9737847

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR003172

The MD-2-related lipid-recognition (ML) domain is implicated in lipid recognition, particularly in the recognition of pathogen related products. It has an immunoglobulin-like beta-sandwich fold similar to that of E-set Ig domains. This domain is present in proteins from plants, animals and fungi, including the following proteins:

  • Epididymal secretory protein E1 (also known as Niemann-Pick C2 protein - Npc2), which is known to bind cholesterol. Niemann-Pick disease type C2 is a fatal hereditary disease characterised by accumulation of low-density lipoprotein-derived cholesterol in lysosomes [ PUBMED:12591954 ].
  • House-dust mite allergen proteins such as Der f 2 from Dermatophagoides farinae and Der p 2 from Dermatophagoides pteronyssinus [ PUBMED:15710415 ].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan LIG (CL0532), which has the following description:

This superfamily includes a number of lipid binding families that have a similar topology to the immunoglobulin fold. The family includes The ML domain Pfam:PF02221. It includes the uncharacterised family Pfam:PF06477.

The clan contains the following 3 members:

DUF1091 E1_DerP2_DerF2 TRP_N


We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

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Curation View help on the curation process

Seed source: Yeats C
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Yeats C
Number in seed: 76
Number in full: 3826
Average length of the domain: 126.40 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 63.80 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 22.7 22.7
Trusted cut-off 22.7 22.7
Noise cut-off 22.6 22.6
Model length: 134
Family (HMM) version: 17
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Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the E1_DerP2_DerF2 domain has been found. There are 77 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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