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1592  structures 7656  species 44  interactions 210543  sequences 988  architectures

Clan: OB (CL0021)

Summary

OB fold Add an annotation

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 45 families and the total number of domains in the clan is 210543. The clan was built by DJ Studholme and A Bateman.

Literature references

  1. Murzin AG; , EMBO J 1993;12:861-867.: OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. PUBMED:8458342 EPMC:8458342

Members

This clan contains the following 45 member families:

BOF CSD DNA_ligase_OB DUF2110 DUF223 DUF3127 DUF35 EFP eIF-1a eIF-5a EutN_CcmL EXOSC1 mRNA_cap_C OB_NTP_bind OB_RNB OmdA Phage_DNA_bind POT1 RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 RNA_pol_Rbc25 RNA_pol_Rpb8 RuvA_N S1 S1-like S1_2 SSB Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TRAM tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind

External database links

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) 46862 (22.3%) View
tRNA_anti-codon (PF01336) 22969 (10.9%) View
CSD (PF00313) 14886 (7.1%) View
TOBE_2 (PF08402) 14426 (6.9%) View
tRNA_bind (PF01588) 10729 (5.1%) View
SSB (PF00436) 10092 (4.8%) View
TRAM (PF01938) 8506 (4.0%) View
Ribosom_S12_S23 (PF00164) 6678 (3.2%) View
Ribosomal_L2 (PF00181) 6547 (3.1%) View
TOBE (PF03459) 5980 (2.8%) View
eIF-1a (PF01176) 5916 (2.8%) View
EFP (PF01132) 5656 (2.7%) View
Ribosomal_S17 (PF00366) 5324 (2.5%) View
OB_RNB (PF08206) 5260 (2.5%) View
OB_NTP_bind (PF07717) 5209 (2.5%) View
DNA_ligase_OB (PF03120) 5111 (2.4%) View
RuvA_N (PF01330) 4290 (2.0%) View
tRNA_anti_2 (PF13742) 4104 (1.9%) View
RecO_N (PF11967) 4019 (1.9%) View
Rho_RNA_bind (PF07497) 3771 (1.8%) View
S1_2 (PF13509) 2158 (1.0%) View
DUF35 (PF01796) 1861 (0.9%) View
BOF (PF04076) 1522 (0.7%) View
continued
Pfam family Num. domains Alignment
EutN_CcmL (PF03319) 1340 (0.6%) View
OmdA (PF13376) 1185 (0.6%) View
TOBE_3 (PF12857) 1134 (0.5%) View
eIF-5a (PF01287) 832 (0.4%) View
DUF223 (PF02721) 441 (0.2%) View
Rep-A_N (PF04057) 381 (0.2%) View
mRNA_cap_C (PF03919) 377 (0.2%) View
RNA_pol_Rpb8 (PF03870) 366 (0.2%) View
EXOSC1 (PF10447) 355 (0.2%) View
POT1 (PF02765) 329 (0.2%) View
RNA_pol_Rbc25 (PF08292) 328 (0.2%) View
Rep_fac-A_3 (PF08661) 305 (0.1%) View
DUF3127 (PF11325) 271 (0.1%) View
tRNA_anti-like (PF12869) 205 (0.1%) View
RecO_N_2 (PF13114) 198 (0.1%) View
S1-like (PF14444) 185 (0.1%) View
Stn1 (PF10451) 123 (0.1%) View
Ten1 (PF12658) 90 (0.0%) View
Ten1_2 (PF15490) 82 (0.0%) View
Phage_DNA_bind (PF02303) 81 (0.0%) View
DUF2110 (PF09883) 44 (0.0%) View
TEBP_beta (PF07404) 15 (0.0%) View
Total: 45 Total: 210543 Clan alignment
 

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Family relationships

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Species distribution

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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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