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8055  structures 10412  species 0  interactions 565227  sequences 4565  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 113 families and the total number of domains in the clan is 565227. 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 113 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 TLP1_add_C 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) 86303 (15.3%) View
tRNA_anti-codon (PF01336) 38516 (6.8%) View
CSD (PF00313) 36091 (6.4%) View
TOBE_2 (PF08402) 24338 (4.3%) View
OB_NTP_bind (PF07717) 22876 (4.0%) View
tRNA_bind (PF01588) 19073 (3.4%) View
SSB (PF00436) 18258 (3.2%) View
TRAM (PF01938) 14024 (2.5%) View
MCM_OB (PF17207) 13573 (2.4%) View
eIF-1a (PF01176) 12645 (2.2%) View
DNA_ligase_A_C (PF04679) 12626 (2.2%) View
Ribosom_S12_S23 (PF00164) 12215 (2.2%) View
Ribosomal_S17 (PF00366) 12173 (2.2%) View
Ribosomal_L2 (PF00181) 11894 (2.1%) View
Prot_ATP_ID_OB (PF16450) 11130 (2.0%) View
OB_MalK (PF17912) 10520 (1.9%) View
EFP (PF01132) 9414 (1.7%) View
Elong-fact-P_C (PF09285) 9379 (1.7%) View
TOBE (PF03459) 9307 (1.6%) View
DNA_ligase_OB (PF03120) 8726 (1.5%) View
RuvA_N (PF01330) 7785 (1.4%) View
Rho_RNA_bind (PF07497) 7592 (1.3%) View
RecO_N (PF11967) 7440 (1.3%) View
NfeD (PF01957) 7215 (1.3%) View
tRNA_anti_2 (PF13742) 7105 (1.3%) View
RecG_wedge (PF17191) 6567 (1.2%) View
RecJ_OB (PF17768) 6395 (1.1%) View
OB_aCoA_assoc (PF01796) 6137 (1.1%) View
CSD2 (PF17876) 5752 (1.0%) View
Rep_fac-A_C (PF08646) 5535 (1.0%) View
TRAM_2 (PF18693) 5440 (1.0%) View
Phage_base_V (PF04717) 5355 (0.9%) View
OB_RNB (PF08206) 4690 (0.8%) View
OB_Dis3 (PF17849) 4380 (0.8%) View
REPA_OB_2 (PF16900) 3553 (0.6%) View
S1_2 (PF13509) 3477 (0.6%) View
CcmE (PF03100) 3331 (0.6%) View
eIF-5a (PF01287) 3027 (0.5%) View
Ribosomal_S4e (PF00900) 2967 (0.5%) View
PCB_OB (PF17092) 2924 (0.5%) View
Rrp44_CSD1 (PF17216) 2838 (0.5%) View
RMI1_N (PF08585) 2693 (0.5%) View
RsgA_N (PF16745) 2618 (0.5%) View
DUF223 (PF02721) 2499 (0.4%) View
Rep-A_N (PF04057) 2422 (0.4%) View
SfsA_N (PF17746) 2394 (0.4%) View
mRNA_cap_C (PF03919) 2130 (0.4%) View
CusF_Ec (PF11604) 2096 (0.4%) View
Ribosomal_S28e (PF01200) 2067 (0.4%) View
Rrp44_S1 (PF17215) 1992 (0.4%) View
RNA_pol_Rpb8 (PF03870) 1964 (0.3%) View
DUF5666 (PF18914) 1819 (0.3%) View
DNA_pol_D_N (PF18018) 1795 (0.3%) View
RNA_pol_Rbc25 (PF08292) 1775 (0.3%) View
POT1 (PF02765) 1738 (0.3%) View
EXOSC1 (PF10447) 1699 (0.3%) View
Rep_fac-A_3 (PF08661) 1627 (0.3%) View
continued
Pfam family Num. domains Alignment
EutN_CcmL (PF03319) 1571 (0.3%) View
Pol_alpha_B_N (PF08418) 1365 (0.2%) View
TOBE_3 (PF12857) 1320 (0.2%) View
Prot_ATP_OB_N (PF17758) 1304 (0.2%) View
POT1PC (PF16686) 1256 (0.2%) View
BRCA-2_OB1 (PF09103) 1201 (0.2%) View
RPA43_OB (PF17875) 1148 (0.2%) View
DNA_ligase_OB_2 (PF14743) 1103 (0.2%) View
DUF3299 (PF11736) 1085 (0.2%) View
DUF3127 (PF11325) 1058 (0.2%) View
RNase_II_C_S1 (PF18614) 1037 (0.2%) View
S1-like (PF14444) 1034 (0.2%) View
HROB (PF15072) 970 (0.2%) View
TLP1_add_C (PF18313) 792 (0.1%) View
TTC5_OB (PF16669) 724 (0.1%) View
CysA_C_terminal (PF17850) 723 (0.1%) View
DUF2815 (PF10991) 721 (0.1%) View
RMI1_C (PF16099) 702 (0.1%) View
Stn1 (PF10451) 685 (0.1%) View
Ten1_2 (PF15490) 679 (0.1%) View
BOF (PF04076) 637 (0.1%) View
DUF1449 (PF07290) 596 (0.1%) View
RMI2 (PF16100) 550 (0.1%) View
MRP-S35 (PF10246) 516 (0.1%) View
WCOB (PF19913) 515 (0.1%) View
TPP1 (PF10341) 495 (0.1%) View
BRCA-2_OB3 (PF09104) 489 (0.1%) View
HIN (PF02760) 484 (0.1%) View
tRNA_anti-like (PF12869) 435 (0.1%) View
CDC24_OB3 (PF17244) 408 (0.1%) View
Gp138_N (PF18352) 403 (0.1%) View
Ten1 (PF12658) 363 (0.1%) View
DUF961 (PF06125) 362 (0.1%) View
CDC24_OB2 (PF17245) 329 (0.1%) View
CDC24_OB1 (PF17246) 314 (0.1%) View
NigD_N (PF12667) 264 (0.0%) View
DUF1344 (PF07076) 254 (0.0%) View
gp32 (PF08804) 248 (0.0%) View
NlpE_C (PF17185) 247 (0.0%) View
Gp5_OB (PF06714) 168 (0.0%) View
DUF6484 (PF20093) 166 (0.0%) View
DNA_ligase_C (PF17879) 161 (0.0%) View
DUF2110 (PF09883) 127 (0.0%) View
RecO_N_2 (PF13114) 75 (0.0%) View
Phage_SSB (PF16773) 56 (0.0%) View
Phage_DNA_bind (PF02303) 53 (0.0%) View
RNA_pol_RpbG (PF16992) 29 (0.0%) View
CDC13_N (PF16853) 26 (0.0%) View
ID (PF18543) 14 (0.0%) View
Cdc13_OB2 (PF18691) 12 (0.0%) View
GlcV_C_terminal (PF17847) 12 (0.0%) View
Fimbrial_PilY2 (PF14481) 8 (0.0%) View
TEBP_beta (PF07404) 8 (0.0%) View
FbpC_C_terminal (PF17845) 5 (0.0%) View
DUF3217 (PF11506) 5 (0.0%) View
ssDBP (PF17878) 1 (0.0%) View
Total: 113 Total: 565227
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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