Summary
OB fold
The OB (oligonucleotide/oligosaccharide binding) was defined by Murzin [1]. The common part of the OB-fold, has a five-stranded beta-sheet coiled to form a closed beta-barrel. This barrel is capped by an alpha-helix located between the third and fourth strands [1].
This clan contains 32 families and the total number of domains in the clan is 69705.
Literature references
- Murzin AG; , EMBO J 1993;12:861-867.: OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. 8458342
Members
This clan contains the following 32 member families:
BOF CSD DNA_ligase_OB DUF2110 DUF223 DUF35 EFP eIF-1a eIF-5a EutN_CcmL EXOSC1 mRNA_cap_C OB_RNB Phage_DNA_bind Rep-A_N Rep_fac-A_3 Rho_RNA_bind Ribosomal_L2 Ribosomal_S12 Ribosomal_S17 RNA_pol_Rbc25 RNA_pol_Rpb8 RuvA_N S1 SSB Stn1 Telo_bind TOBE TOBE_2 TRAM tRNA_anti tRNA_bindExternal database links
| CATH: | 2.40.50.140 |
| SCOP: | 50249 |
Domain organisation
Below is a listing of the unique domain organisations or architectures from this clan. More...
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Alignments
The table below shows the number of occurrences of each domain throughout the sequence database. More...
| Pfam family | Num. domains | Alignment |
|---|---|---|
| S1 (PF00575) | 16404 (23.5%) | View |
| tRNA_anti (PF01336) | 9423 (13.5%) | View |
| TOBE_2 (PF08402) | 5452 (7.8%) | View |
| CSD (PF00313) | 5422 (7.8%) | View |
| tRNA_bind (PF01588) | 3662 (5.3%) | View |
| SSB (PF00436) | 3508 (5.0%) | View |
| TRAM (PF01938) | 3059 (4.4%) | View |
| Ribosomal_S12 (PF00164) | 2579 (3.7%) | View |
| Ribosomal_L2 (PF00181) | 2478 (3.6%) | View |
| eIF-1a (PF01176) | 2260 (3.2%) | View |
| TOBE (PF03459) | 2126 (3.0%) | View |
| Ribosomal_S17 (PF00366) | 1940 (2.8%) | View |
| EFP (PF01132) | 1881 (2.7%) | View |
| OB_RNB (PF08206) | 1699 (2.4%) | View |
| DNA_ligase_OB (PF03120) | 1692 (2.4%) | View |
| RuvA_N (PF01330) | 1451 (2.1%) | View |
| Rho_RNA_bind (PF07497) | 1327 (1.9%) | View |
| continued | ||
| Pfam family | Num. domains | Alignment |
|---|---|---|
| DUF35 (PF01796) | 730 (1.0%) | View |
| EutN_CcmL (PF03319) | 445 (0.6%) | View |
| eIF-5a (PF01287) | 421 (0.6%) | View |
| BOF (PF04076) | 420 (0.6%) | View |
| Telo_bind (PF02765) | 167 (0.2%) | View |
| mRNA_cap_C (PF03919) | 167 (0.2%) | View |
| EXOSC1 (PF10447) | 163 (0.2%) | View |
| RNA_pol_Rpb8 (PF03870) | 163 (0.2%) | View |
| Rep-A_N (PF04057) | 154 (0.2%) | View |
| Rep_fac-A_3 (PF08661) | 149 (0.2%) | View |
| RNA_pol_Rbc25 (PF08292) | 146 (0.2%) | View |
| DUF223 (PF02721) | 131 (0.2%) | View |
| Phage_DNA_bind (PF02303) | 44 (0.1%) | View |
| DUF2110 (PF09883) | 24 (0.0%) | View |
| Stn1 (PF10451) | 18 (0.0%) | View |
| Total: 32 | Total: 69705 | 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
HideThis tree shows the occurrence of the domains in this clan across different species. More...
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Interactions
There are 44 interactions for this clan. More...
Structures
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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