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7445  structures 10206  species 0  interactions 533742  sequences 4475  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 112 families and the total number of domains in the clan is 533742. 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 112 member families:

BOF BRCA-2_OB1 BRCA-2_OB3 CcmE CDC13_N Cdc13_OB2 CDC24_OB1 CDC24_OB2 CDC24_OB3 CSD CSD2 CusF_Ec CysA_C_terminal DNA_ligase_A_C DNA_ligase_C DNA_ligase_OB DNA_ligase_OB_2 DNA_pol_D_N DUF1344 DUF1449 DUF2110 DUF223 DUF2815 DUF3127 DUF3217 DUF3299 DUF5666 DUF6484 DUF961 EFP eIF-1a eIF-5a Elong-fact-P_C EutN_CcmL EXOSC1 FbpC_C_terminal Fimbrial_PilY2 GlcV_C_terminal Gp138_N gp32 Gp5_OB HIN HROB ID MCM_OB mRNA_cap_C MRP-S35 NfeD NigD_N NlpE_C OB_aCoA_assoc OB_Dis3 OB_MalK OB_NTP_bind OB_RNB PCB_OB Phage_base_V Phage_DNA_bind Phage_SSB Pol_alpha_B_N POT1 POT1PC Prot_ATP_ID_OB Prot_ATP_OB_N RecG_wedge RecJ_OB RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 Rep_fac-A_C REPA_OB_2 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 Ribosomal_S28e Ribosomal_S4e RMI1_C RMI1_N RMI2 RNA_pol_Rbc25 RNA_pol_Rpb8 RNA_pol_RpbG RNase_II_C_S1 RPA43_OB Rrp44_CSD1 Rrp44_S1 RsgA_N RuvA_N S1 S1-like S1_2 SfsA_N SSB ssDBP Stn1 TEBP_beta Ten1 Ten1_2 TOBE TOBE_2 TOBE_3 TPP1 TRAM TRAM_2 tRNA_anti-codon tRNA_anti-like tRNA_anti_2 tRNA_bind TTC5_OB WCOB

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) 83503 (15.6%) View
tRNA_anti-codon (PF01336) 36374 (6.8%) View
CSD (PF00313) 33379 (6.3%) View
TOBE_2 (PF08402) 23214 (4.3%) View
OB_NTP_bind (PF07717) 20489 (3.8%) View
tRNA_bind (PF01588) 18319 (3.4%) View
SSB (PF00436) 17716 (3.3%) View
TRAM (PF01938) 13394 (2.5%) View
MCM_OB (PF17207) 12340 (2.3%) View
eIF-1a (PF01176) 11946 (2.2%) View
DNA_ligase_A_C (PF04679) 11751 (2.2%) View
Ribosom_S12_S23 (PF00164) 11673 (2.2%) View
Ribosomal_S17 (PF00366) 11559 (2.2%) View
Ribosomal_L2 (PF00181) 11314 (2.1%) View
Prot_ATP_ID_OB (PF16450) 10403 (1.9%) View
OB_MalK (PF17912) 10038 (1.9%) View
EFP (PF01132) 9072 (1.7%) View
Elong-fact-P_C (PF09285) 9007 (1.7%) View
TOBE (PF03459) 8860 (1.7%) View
DNA_ligase_OB (PF03120) 8386 (1.6%) View
RuvA_N (PF01330) 7477 (1.4%) View
Rho_RNA_bind (PF07497) 7319 (1.4%) View
RecO_N (PF11967) 7237 (1.4%) View
NfeD (PF01957) 6901 (1.3%) View
tRNA_anti_2 (PF13742) 6822 (1.3%) View
RecG_wedge (PF17191) 6435 (1.2%) View
RecJ_OB (PF17768) 6144 (1.2%) View
OB_aCoA_assoc (PF01796) 5857 (1.1%) View
CSD2 (PF17876) 5526 (1.0%) View
TRAM_2 (PF18693) 5218 (1.0%) View
Phage_base_V (PF04717) 5156 (1.0%) View
Rep_fac-A_C (PF08646) 4772 (0.9%) View
OB_RNB (PF08206) 4572 (0.9%) View
OB_Dis3 (PF17849) 3928 (0.7%) View
S1_2 (PF13509) 3376 (0.6%) View
REPA_OB_2 (PF16900) 3196 (0.6%) View
CcmE (PF03100) 3176 (0.6%) View
eIF-5a (PF01287) 2787 (0.5%) View
PCB_OB (PF17092) 2782 (0.5%) View
Ribosomal_S4e (PF00900) 2738 (0.5%) View
RsgA_N (PF16745) 2540 (0.5%) View
Rrp44_CSD1 (PF17216) 2483 (0.5%) View
RMI1_N (PF08585) 2438 (0.5%) View
SfsA_N (PF17746) 2309 (0.4%) View
DUF223 (PF02721) 2203 (0.4%) View
Rep-A_N (PF04057) 2186 (0.4%) View
CusF_Ec (PF11604) 2046 (0.4%) View
mRNA_cap_C (PF03919) 1936 (0.4%) View
Ribosomal_S28e (PF01200) 1932 (0.4%) View
RNA_pol_Rpb8 (PF03870) 1821 (0.3%) View
Rrp44_S1 (PF17215) 1785 (0.3%) View
DUF5666 (PF18914) 1740 (0.3%) View
DNA_pol_D_N (PF18018) 1676 (0.3%) View
RNA_pol_Rbc25 (PF08292) 1623 (0.3%) View
POT1 (PF02765) 1608 (0.3%) View
EXOSC1 (PF10447) 1557 (0.3%) View
Rep_fac-A_3 (PF08661) 1515 (0.3%) View
continued
Pfam family Num. domains Alignment
EutN_CcmL (PF03319) 1509 (0.3%) View
Prot_ATP_OB_N (PF17758) 1257 (0.2%) View
Pol_alpha_B_N (PF08418) 1255 (0.2%) View
TOBE_3 (PF12857) 1254 (0.2%) View
POT1PC (PF16686) 1142 (0.2%) View
BRCA-2_OB1 (PF09103) 1064 (0.2%) View
DUF3299 (PF11736) 1056 (0.2%) View
DNA_ligase_OB_2 (PF14743) 1049 (0.2%) View
DUF3127 (PF11325) 1027 (0.2%) View
RNase_II_C_S1 (PF18614) 998 (0.2%) View
S1-like (PF14444) 919 (0.2%) View
RPA43_OB (PF17875) 882 (0.2%) View
HROB (PF15072) 865 (0.2%) View
CysA_C_terminal (PF17850) 708 (0.1%) View
DUF2815 (PF10991) 672 (0.1%) View
Stn1 (PF10451) 634 (0.1%) View
TTC5_OB (PF16669) 628 (0.1%) View
Ten1_2 (PF15490) 612 (0.1%) View
RMI1_C (PF16099) 606 (0.1%) View
BOF (PF04076) 592 (0.1%) View
DUF1449 (PF07290) 572 (0.1%) View
RMI2 (PF16100) 479 (0.1%) View
MRP-S35 (PF10246) 435 (0.1%) View
HIN (PF02760) 425 (0.1%) View
tRNA_anti-like (PF12869) 415 (0.1%) View
WCOB (PF19913) 413 (0.1%) View
TPP1 (PF10341) 410 (0.1%) View
Gp138_N (PF18352) 388 (0.1%) View
BRCA-2_OB3 (PF09104) 384 (0.1%) View
CDC24_OB3 (PF17244) 370 (0.1%) View
Ten1 (PF12658) 360 (0.1%) View
DUF961 (PF06125) 350 (0.1%) View
CDC24_OB2 (PF17245) 306 (0.1%) View
CDC24_OB1 (PF17246) 289 (0.1%) View
NigD_N (PF12667) 256 (0.0%) View
DUF1344 (PF07076) 244 (0.0%) View
gp32 (PF08804) 240 (0.0%) View
NlpE_C (PF17185) 238 (0.0%) View
DUF6484 (PF20093) 168 (0.0%) View
Gp5_OB (PF06714) 162 (0.0%) View
DNA_ligase_C (PF17879) 146 (0.0%) View
DUF2110 (PF09883) 122 (0.0%) View
RecO_N_2 (PF13114) 70 (0.0%) View
Phage_SSB (PF16773) 61 (0.0%) View
Phage_DNA_bind (PF02303) 52 (0.0%) View
RNA_pol_RpbG (PF16992) 28 (0.0%) View
CDC13_N (PF16853) 24 (0.0%) View
GlcV_C_terminal (PF17847) 11 (0.0%) View
Cdc13_OB2 (PF18691) 10 (0.0%) View
Fimbrial_PilY2 (PF14481) 8 (0.0%) View
TEBP_beta (PF07404) 7 (0.0%) View
ID (PF18543) 5 (0.0%) View
FbpC_C_terminal (PF17845) 5 (0.0%) View
DUF3217 (PF11506) 5 (0.0%) View
ssDBP (PF17878) 1 (0.0%) View
Total: 112 Total: 533742
No alignment ℹ
 

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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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