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312  structures 5344  species 4  interactions 38636  sequences 491  architectures

Clan: KH (CL0007)


K-Homology (KH) domain Superfamily Add an annotation

The KH domain is thought to be the second most prevalent RNA binding motif in proteins. The motif is characterised by a conserved GXXXGXXG in the middle of the domain. Structures of KH reveal that the KH domain is arranged as either a beta-alpha-alpha-beta-beta (mini-KH domain) or beta-alpha-alpha-beta-beta-alpha (maxi-KH domain). The secondary elements are separated by at least four loop segments. The second loop is located between beta-1 and al The KH domain can be found either as single or multiple copies. The KH domain usually binds RNA as a multimer.

This clan contains 5 families and the total number of domains in the clan is 38636. The clan was built by RD Finn.


This clan contains the following 5 member families:

KH_1 KH_2 KH_3 KH_4 KH_5

External database links

Domain organisation

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

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

Pfam family Num. domains Alignment
KH_1 (PF00013) 19558 (50.6%) View
KH_2 (PF07650) 9989 (25.9%) View
KH_5 (PF13184) 4542 (11.8%) View
KH_4 (PF13083) 3577 (9.3%) View
KH_3 (PF13014) 970 (2.5%) View
Total: 5 Total: 38636 Clan alignment

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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...



There are 4 interactions for this clan. More...

Interacting families
KH_1 KH_1


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.

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