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1515  structures 23515  species 150  interactions 903287  sequences 1389  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 49 families and the total number of domains in the clan is 903287. 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 49 member families:

BOF CSD DNA_ligase_OB DUF2110 DUF223 DUF3127 EFP eIF-1a eIF-5a EutN_CcmL EXOSC1 mRNA_cap_C OB_aCoA_assoc OB_NTP_bind OB_RNB PCB_OB Phage_DNA_bind POT1 RecO_N RecO_N_2 Rep-A_N Rep_fac-A_3 REPA_OB_2 Rho_RNA_bind Ribosom_S12_S23 Ribosomal_L2 Ribosomal_S17 RNA_pol_Rbc25 RNA_pol_Rpb8 RNA_pol_RpbG RsgA_N RuvA_N S1 S1-like S1_2 SSB SSL_OB 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) 190207 (21.1%) View
tRNA_anti-codon (PF01336) 83695 (9.3%) View
CSD (PF00313) 66210 (7.3%) View
TOBE_2 (PF08402) 56376 (6.2%) View
SSB (PF00436) 48179 (5.3%) View
tRNA_bind (PF01588) 46630 (5.2%) View
SSL_OB (PF09199) 40364 (4.5%) View
TRAM (PF01938) 33818 (3.7%) View
OB_RNB (PF08206) 25743 (2.8%) View
TOBE (PF03459) 25531 (2.8%) View
EFP (PF01132) 23549 (2.6%) View
DNA_ligase_OB (PF03120) 22503 (2.5%) View
Ribosom_S12_S23 (PF00164) 22460 (2.5%) View
Ribosomal_L2 (PF00181) 22290 (2.5%) View
eIF-1a (PF01176) 21549 (2.4%) View
Ribosomal_S17 (PF00366) 20644 (2.3%) View
RuvA_N (PF01330) 18665 (2.1%) View
tRNA_anti_2 (PF13742) 18266 (2.0%) View
RecO_N (PF11967) 17883 (2.0%) View
Rho_RNA_bind (PF07497) 17169 (1.9%) View
OB_NTP_bind (PF07717) 13107 (1.5%) View
OB_aCoA_assoc (PF01796) 10986 (1.2%) View
S1_2 (PF13509) 10019 (1.1%) View
BOF (PF04076) 9075 (1.0%) View
RsgA_N (PF16745) 7931 (0.9%) View
continued
Pfam family Num. domains Alignment
PCB_OB (PF17092) 6877 (0.8%) View
TOBE_3 (PF12857) 6477 (0.7%) View
EutN_CcmL (PF03319) 6090 (0.7%) View
eIF-5a (PF01287) 1378 (0.2%) View
REPA_OB_2 (PF16900) 1147 (0.1%) View
DUF3127 (PF11325) 741 (0.1%) View
mRNA_cap_C (PF03919) 737 (0.1%) View
Rep-A_N (PF04057) 729 (0.1%) View
POT1 (PF02765) 717 (0.1%) View
RNA_pol_Rpb8 (PF03870) 689 (0.1%) View
DUF223 (PF02721) 641 (0.1%) View
RNA_pol_Rbc25 (PF08292) 624 (0.1%) View
EXOSC1 (PF10447) 614 (0.1%) View
Rep_fac-A_3 (PF08661) 599 (0.1%) View
tRNA_anti-like (PF12869) 568 (0.1%) View
RecO_N_2 (PF13114) 495 (0.1%) View
S1-like (PF14444) 339 (0.0%) View
Stn1 (PF10451) 263 (0.0%) View
Ten1_2 (PF15490) 183 (0.0%) View
Ten1 (PF12658) 172 (0.0%) View
Phage_DNA_bind (PF02303) 154 (0.0%) View
DUF2110 (PF09883) 141 (0.0%) View
RNA_pol_RpbG (PF16992) 45 (0.0%) View
TEBP_beta (PF07404) 18 (0.0%) View
Total: 49 Total: 903287 Clan alignment
 

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Family relationships

This diagram shows the relationships between members of this clan. More...

We could not retrieve a family relationship diagram for this clan.

Species distribution

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Interactions

There are 150 interactions for this clan. More...

Interacting families
A B
A2M SSL_OB
ABC_tran TOBE_2
C1-set SSL_OB
CSD CSD
S1
zf-CCHC
DEAD OB_NTP_bind
DNA_ligase_aden DNA_ligase_OB
DNA_ligase_OB DNA_ligase_ZBD
HHH_2
HHH_5
DUF1743 tRNA_anti-codon
DUF4479 tRNA_bind
EFG_II Ribosom_S12_S23
EFP Elong-fact-P_C
EFP_N EFP
eIF-5a
eIF-1a eIF-1a
Ribosomal_S15
eIF-5a EFP_N
eIF-5a
EutN_CcmL EutN_CcmL
GTP_EFTU_D2 Ribosom_S12_S23
HA2 OB_NTP_bind
Helicase_C OB_NTP_bind
IF-2 eIF-1a
Ig_2 SSL_OB
KH_1 S1
KOW Ribosomal_S17
mRNA_cap_C mRNA_cap_C
mRNA_cap_enzyme
mRNA_cap_enzyme mRNA_cap_C
mRNA_triPase mRNA_cap_C
Phage_DNA_bind Phage_DNA_bind
POT1 POT1
TEBP_beta
RecO_C RecO_N
RecO_N RecO_C
Rep_fac-A_3 Rep_fac-A_3
Rep_fac-A_C
RPA_C
tRNA_anti-codon
RF-1 Ribosom_S12_S23
Rho_N Rho_RNA_bind
Rho_RNA_bind ATP-synt_ab
Rho_N
Ribosom_S12_S23 Cytotoxic
EFG_II
EFG_IV
eIF-1a
GTP_EFTU_D2
ParE_toxin
RF-1
Ribosomal_L18e
Ribosomal_S13_N
Ribosomal_S17
Ribosomal_S30
Ribosomal_S8
RRF
RS4NT
S4
Ribosomal_L10 Ribosomal_L2
Ribosomal_L13e Ribosomal_L2
Ribosomal_L18ae Ribosomal_L2
Ribosomal_L18e Ribosomal_L2
Ribosomal_L2 Ribosomal_L10
Ribosomal_L15e
Ribosomal_L18e
Ribosomal_L2
Ribosomal_L23eN
Ribosomal_L28e
Ribosomal_L2_C
Ribosomal_L30_N
Ribosomal_L32e
Ribosomal_L34e
Ribosomal_L37ae
Ribosomal_L4
Ribosomal_L44
Ribosomal_L6e_N
Ribosomal_L9_C
Ribosomal_S24e
Ribosomal_L27e Ribosomal_L2
Ribosomal_L33 Ribosomal_L2
Ribosomal_L36 Ribosomal_L2
Ribosomal_L37ae Ribosomal_L2
Ribosomal_L39 Ribosomal_L2
Ribosomal_S13_N eIF-1a
Ribosomal_S15 Ribosomal_S17
Ribosomal_S17 Ribosom_S12_S23
Ribosomal_S8
Ribosomal_S8e
Ribosomal_S30 eIF-1a
Ribosomal_S8 Ribosom_S12_S23
Ribosomal_S17
Ribosomal_S8e Ribosomal_S17
RNA_pol_L RNA_pol_Rpb8
RNA_pol_Rpb1_3 RNA_pol_Rpb8
RNA_pol_Rpb1_4 RNA_pol_Rpb8
RNA_pol_Rpb1_5 RNA_pol_Rpb8
RNA_pol_Rpb1_6 RNA_pol_Rpb8
RNA_pol_Rpb2_6 RNA_pol_Rpb8
RNA_pol_Rpb2_7 S1
RNA_pol_Rpb4 RNA_pol_Rbc25
S1
RNA_pol_Rpb8 RNA_pol_L_2
RNase_E_G S1
RNase_PH EXOSC1
S1
RNB S1
RPA_C Rep_fac-A_3
RuvA_C RuvA_N
RuvA_N HHH_5
RuvA_C
RuvA_N
S1 CSD
EIF_2_alpha
KH_1
Pkinase
RNA_pol_Rpb4
RNA_pol_Rpb8
RNase_E_G
RNase_PH
S1
SHS2_Rpb7-N RNA_pol_Rbc25
S1
SmpB Ribosom_S12_S23
SSB SSB
SSL_OB SSL_OB
Stap_Strp_tox_C
Stap_Strp_tox_C SSL_OB
Stn1 Ten1
SUI1 Ribosom_S12_S23
Ribosomal_S17
Ten1 Stn1
TOBE TOBE
TOBE_2 PTS_EIIA_1
TOBE_2
TRAM tRNA_U5-meth_tr
tRNA-synt_2 tRNA_anti-codon
tRNA_anti-codon DNA_pol3_alpha
Rep_fac-A_3
Rep_fac-A_C
STN1_2
tRNA-synt_2
tRNA_anti-codon
tRNA_anti-like tRNA_anti-like
tRNA_bind B3_4
DUF4479
tRNA_bind
zf-CCHC CSD

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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