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1420  structures 8857  species 0  interactions 131788  sequences 1084  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 14 families and the total number of domains in the clan is 131788. The clan was built by RD Finn.


This clan contains the following 14 member families:

DUF2096 DUF370 KH_1 KH_10 KH_2 KH_4 KH_5 KH_6 KH_7 KH_8 KH_9 MOEP19 MRP-S24 SLS

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) 89567 (68.0%) View
KH_2 (PF07650) 18393 (14.0%) View
KH_5 (PF13184) 7799 (5.9%) View
KH_4 (PF13083) 5631 (4.3%) View
KH_6 (PF15985) 2749 (2.1%) View
KH_8 (PF17903) 2100 (1.6%) View
DUF370 (PF04025) 2067 (1.6%) View
KH_9 (PF17904) 1751 (1.3%) View
SLS (PF14611) 531 (0.4%) View
MRP-S24 (PF14955) 428 (0.3%) View
MOEP19 (PF16005) 425 (0.3%) View
KH_7 (PF17214) 285 (0.2%) View
KH_10 (PF17905) 35 (0.0%) View
DUF2096 (PF09869) 27 (0.0%) View
Total: 14 Total: 131788 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...



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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