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4871  structures 10712  species 187  interactions 466217  sequences 3221  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 107 families and the total number of domains in the clan is 466217. 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 107 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 DUF4539 DUF961 EFP eIF-1a eIF-5a Elong-fact-P_C EutN_CcmL EXOSC1 FbpC_C_terminal Fimbrial_PilY2 GlcV_C_terminal Gp138_N gp32 HIN 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_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

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) 77742 (16.7%) View
tRNA_anti-codon (PF01336) 33571 (7.2%) View
CSD (PF00313) 28162 (6.0%) View
TOBE_2 (PF08402) 21352 (4.6%) View
tRNA_bind (PF01588) 17216 (3.7%) View
SSB (PF00436) 16249 (3.5%) View
OB_NTP_bind (PF07717) 13623 (2.9%) View
TRAM (PF01938) 12625 (2.7%) View
eIF-1a (PF01176) 11256 (2.4%) View
Ribosomal_S17 (PF00366) 10926 (2.3%) View
Ribosom_S12_S23 (PF00164) 10822 (2.3%) View
Ribosomal_L2 (PF00181) 10679 (2.3%) View
DNA_ligase_A_C (PF04679) 9664 (2.1%) View
OB_MalK (PF17912) 9544 (2.0%) View
Elong-fact-P_C (PF09285) 9037 (1.9%) View
EFP (PF01132) 8909 (1.9%) View
TOBE (PF03459) 8827 (1.9%) View
MCM_OB (PF17207) 8585 (1.8%) View
DNA_ligase_OB (PF03120) 8213 (1.8%) View
RuvA_N (PF01330) 7590 (1.6%) View
RecO_N (PF11967) 7486 (1.6%) View
Prot_ATP_ID_OB (PF16450) 7378 (1.6%) View
Rho_RNA_bind (PF07497) 6817 (1.5%) View
RecJ_OB (PF17768) 6499 (1.4%) View
RecG_wedge (PF17191) 6490 (1.4%) View
tRNA_anti_2 (PF13742) 6452 (1.4%) View
NfeD (PF01957) 6423 (1.4%) View
OB_aCoA_assoc (PF01796) 5824 (1.2%) View
CSD2 (PF17876) 5401 (1.2%) View
TRAM_2 (PF18693) 4769 (1.0%) View
OB_RNB (PF08206) 4539 (1.0%) View
S1_2 (PF13509) 3246 (0.7%) View
Rep_fac-A_C (PF08646) 2952 (0.6%) View
CcmE (PF03100) 2926 (0.6%) View
PCB_OB (PF17092) 2701 (0.6%) View
OB_Dis3 (PF17849) 2549 (0.5%) View
RsgA_N (PF16745) 2402 (0.5%) View
SfsA_N (PF17746) 2241 (0.5%) View
CusF_Ec (PF11604) 2175 (0.5%) View
REPA_OB_2 (PF16900) 2107 (0.5%) View
Ribosomal_S4e (PF00900) 2069 (0.4%) View
eIF-5a (PF01287) 1958 (0.4%) View
RMI1_N (PF08585) 1735 (0.4%) View
Ribosomal_S28e (PF01200) 1524 (0.3%) View
Rrp44_CSD1 (PF17216) 1460 (0.3%) View
EutN_CcmL (PF03319) 1434 (0.3%) View
Rep-A_N (PF04057) 1328 (0.3%) View
TOBE_3 (PF12857) 1308 (0.3%) View
mRNA_cap_C (PF03919) 1286 (0.3%) View
RNA_pol_Rpb8 (PF03870) 1246 (0.3%) View
DNA_pol_D_N (PF18018) 1190 (0.3%) View
RNA_pol_Rbc25 (PF08292) 1136 (0.2%) View
EXOSC1 (PF10447) 1109 (0.2%) View
Rrp44_S1 (PF17215) 1087 (0.2%) View
continued
Pfam family Num. domains Alignment
Rep_fac-A_3 (PF08661) 1077 (0.2%) View
POT1 (PF02765) 1073 (0.2%) View
DUF223 (PF02721) 1044 (0.2%) View
Prot_ATP_OB_N (PF17758) 1037 (0.2%) View
DUF3299 (PF11736) 1009 (0.2%) View
DUF3127 (PF11325) 913 (0.2%) View
DNA_ligase_OB_2 (PF14743) 902 (0.2%) View
RNase_II_C_S1 (PF18614) 811 (0.2%) View
Pol_alpha_B_N (PF08418) 799 (0.2%) View
POT1PC (PF16686) 754 (0.2%) View
BOF (PF04076) 703 (0.2%) View
BRCA-2_OB1 (PF09103) 683 (0.1%) View
CysA_C_terminal (PF17850) 674 (0.1%) View
RPA43_OB (PF17875) 630 (0.1%) View
DUF1449 (PF07290) 563 (0.1%) View
DUF2815 (PF10991) 512 (0.1%) View
S1-like (PF14444) 507 (0.1%) View
DUF4539 (PF15072) 479 (0.1%) View
Stn1 (PF10451) 444 (0.1%) View
RMI1_C (PF16099) 401 (0.1%) View
tRNA_anti-like (PF12869) 388 (0.1%) View
TTC5_OB (PF16669) 368 (0.1%) View
DUF961 (PF06125) 338 (0.1%) View
Ten1_2 (PF15490) 333 (0.1%) View
MRP-S35 (PF10246) 326 (0.1%) View
Gp138_N (PF18352) 325 (0.1%) View
NigD_N (PF12667) 279 (0.1%) View
DUF1344 (PF07076) 267 (0.1%) View
RMI2 (PF16100) 264 (0.1%) View
Ten1 (PF12658) 261 (0.1%) View
TPP1 (PF10341) 247 (0.1%) View
BRCA-2_OB3 (PF09104) 243 (0.1%) View
HIN (PF02760) 227 (0.0%) View
CDC24_OB3 (PF17244) 223 (0.0%) View
NlpE_C (PF17185) 214 (0.0%) View
CDC24_OB1 (PF17246) 171 (0.0%) View
CDC24_OB2 (PF17245) 171 (0.0%) View
gp32 (PF08804) 158 (0.0%) View
DUF2110 (PF09883) 158 (0.0%) View
RecO_N_2 (PF13114) 88 (0.0%) View
DNA_ligase_C (PF17879) 86 (0.0%) View
Phage_DNA_bind (PF02303) 46 (0.0%) View
ID (PF18543) 42 (0.0%) View
Phage_SSB (PF16773) 35 (0.0%) View
RNA_pol_RpbG (PF16992) 30 (0.0%) View
CDC13_N (PF16853) 29 (0.0%) View
Cdc13_OB2 (PF18691) 15 (0.0%) View
GlcV_C_terminal (PF17847) 10 (0.0%) View
TEBP_beta (PF07404) 7 (0.0%) View
DUF3217 (PF11506) 5 (0.0%) View
FbpC_C_terminal (PF17845) 4 (0.0%) View
Fimbrial_PilY2 (PF14481) 4 (0.0%) View
ssDBP (PF17878) 1 (0.0%) View
Total: 107 Total: 466217
No alignment ℹ
 

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Family relationships

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

Species distribution

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Interactions

There are 187 interactions for this clan. More...

Interacting families
A B
ABC_tran TOBE_2
BRCA-2_helical BRCA-2_OB1
CSD CSD
S1
zf-CCHC
DEAD OB_NTP_bind
DNA_ligase_A_C DNA_ligase_A_M
DNA_ligase_A_M DNA_ligase_A_C
DNA_ligase_OB_2
DNA_ligase_A_N DNA_ligase_A_C
DNA_ligase_aden DNA_ligase_OB
DNA_ligase_OB DNA_ligase_ZBD
HHH_2
HHH_5
DNA_ligase_OB_2 DNA_ligase_A_M
DNA_ligase_OB_2
DSS1_SEM1 BRCA-2_OB1
DUF1743 tRNA_anti-codon
DUF3217 DUF3217
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
Elong-fact-P_C EFP_N
Elong-fact-P_C
EutN_CcmL EutN_CcmL
Fimbrial_PilY2 Fimbrial_PilY2
gp32 gp32
GTP_EFTU_D2 Ribosom_S12_S23
HA2 OB_NTP_bind
Helicase_C OB_NTP_bind
HIN HIN
IF-2 eIF-1a
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
NigD_N NigD_N
Phage_DNA_bind Phage_DNA_bind
Pol_alpha_B_N DNA_pol_E_B
Pol_alpha_B_N
zf-DNA_Pol
Polyoma_lg_T_C Pol_alpha_B_N
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_L27A
Ribosomal_S13_N
Ribosomal_S17
Ribosomal_S30
Ribosomal_S8
RRF
RS4NT
S4
Ribosomal_L10 Ribosomal_L2
Ribosomal_L13e Ribosomal_L2
Ribosomal_L18A Ribosomal_L2
Ribosomal_L2 Ribosomal_L10
Ribosomal_L15e
Ribosomal_L2
Ribosomal_L23eN
Ribosomal_L27A
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_L27A Ribosomal_L2
Ribosomal_L27e Ribosomal_L2
Ribosomal_L33 Ribosomal_L2
Ribosomal_L36 Ribosomal_L2
Ribosomal_L37ae Ribosomal_L2
Ribosomal_L39 Ribosomal_L2
Ribosomal_S11 Ribosomal_S28e
Ribosomal_S13_N eIF-1a
Ribosomal_S15 Ribosomal_S17
Ribosomal_S17 Ribosom_S12_S23
Ribosomal_S8
Ribosomal_S8e
Ribosomal_S2 Ribosomal_S28e
Ribosomal_S21e Ribosomal_S28e
Ribosomal_S26e Ribosomal_S28e
Ribosomal_S27 Ribosomal_S28e
Ribosomal_S28e Ribosomal_S11
Ribosomal_S21e
Ribosomal_S26e
Ribosomal_S27
Ribosomal_S5
Ribosomal_S7
Ribosomal_S30 eIF-1a
Ribosomal_S4e
Ribosomal_S4e KH_2
KOW
WD40
Ribosomal_S7 Elong-fact-P_C
Ribosomal_S28e
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
Rep_fac-A_C
RS4NT Ribosomal_S4e
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
S4 Ribosomal_S4e
SHS2_Rpb7-N RNA_pol_Rbc25
S1
SmpB Ribosom_S12_S23
SSB SSB
Stn1 Ten1
SUI1 Ribosom_S12_S23
Ribosomal_S17
Ten1 Stn1
TOBE TOBE
TOBE_2 PTS_EIIA_1
TOBE_2
Tower BRCA-2_OB3
TPP1 TPP1
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
ubiquitin Ribosomal_S28e
zf-CCHC CSD
zf-DNA_Pol Pol_alpha_B_N

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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