4DR7

Crystal structure of the Thermus thermophilus (HB8) 30S ribosomal subunit with codon, crystallographically disordered near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position, and streptomycin bound


ChainDomainClassArchitectureTopologyHomology
3.40.50.10490 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Glucose-6-phosphate isomerase like protein
3.40.50.10490 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Glucose-6-phosphate isomerase like protein
1.10.287.610 Mainly Alpha Orthogonal Bundle Helix Hairpins Helix hairpin bin
3.30.300.20 Alpha Beta 2-Layer Sandwich GMP Synthetase Chain A, domain 3
3.30.1140.32 Alpha Beta 2-Layer Sandwich Ribosomal protein S3 C-terminal domain Ribosomal protein S3, C-terminal domain
1.10.1050.10 Mainly Alpha Orthogonal Bundle Ribosomal Protein S4 Delta 41 Chain A, domain 1
1.10.1050.10 Mainly Alpha Orthogonal Bundle Ribosomal Protein S4 Delta 41 Chain A, domain 1
3.10.290.10 Alpha Beta Roll Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region Chain A
3.30.160.20 Alpha Beta 2-Layer Sandwich Double Stranded RNA Binding Domain
3.30.230.10 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5 domain 2
3.30.70.60 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Ribosomal protein S6/Translation elongation factor EF1B
1.10.455.10 Mainly Alpha Orthogonal Bundle Ribosomal Protein S7 Ribosomal protein S7/S5
3.30.1370.30 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8 Chain: A, domain 1
3.30.1490.10 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1
3.30.230.10 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5 domain 2
3.30.70.600 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits Ribosomal protein S10
3.30.420.80 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase domain 5
2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
1.10.8.50 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein domain 3
4.10.910.10 Few Secondary Structures Irregular 30s ribosomal protein s13 domain 2
4.10.830.10 Few Secondary Structures Irregular 30s Ribosomal Protein S14 Chain N
1.10.287.10 Mainly Alpha Orthogonal Bundle Helix Hairpins S15/NS1, RNA-binding
3.30.1320.10 Alpha Beta 2-Layer Sandwich S16 Ribosomal Protein Chain: A
2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
4.10.640.10 Few Secondary Structures Irregular 30s Ribosomal Protein S18 Ribosomal protein S18
3.30.860.10 Alpha Beta 2-Layer Sandwich 30s Ribosomal Protein S19 Chain A
1.20.58.110 Mainly Alpha Up-down Bundle Methane Monooxygenase Hydroxylase Chain G, domain 1

Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
PF00318Ribosomal protein S2 (Ribosomal_S2)Ribosomal protein S2- Family
PF07650KH domain (KH_2)KH domain- Domain
PF00189Ribosomal protein S3, C-terminal domain (Ribosomal_S3_C)Ribosomal protein S3, C-terminal domainThis family contains a central domain Pfam:PF00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer.Domain
PF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
PF01479S4 domain (S4)S4 domainThe S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.
Domain
PF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domain- Domain
PF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domain- Domain
PF01250Ribosomal protein S6 (Ribosomal_S6)Ribosomal protein S6- Domain
PF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
PF00338Ribosomal protein S10p/S20e (Ribosomal_S10)Ribosomal protein S10p/S20eThis family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.Domain
PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
PF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
PF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- Family
PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
PF00886Ribosomal protein S16 (Ribosomal_S16)Ribosomal protein S16- Family
PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
PF01084Ribosomal protein S18 (Ribosomal_S18)Ribosomal protein S18- Family
PF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19- Domain
PF01649Ribosomal protein S20 (Ribosomal_S20p)Ribosomal protein S20- Family
PF1707030S ribosomal protein Thx (Thx)30S ribosomal protein Thx- Family

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
16S rRNAnonenonenone
30S ribosomal protein S2
    30S ribosomal protein S3
      30S ribosomal protein S4
        30S ribosomal protein S5
          30S ribosomal protein S6
            30S ribosomal protein S7
              30S ribosomal protein S8
                30S ribosomal protein S9
                  30S ribosomal protein S10
                    30S ribosomal protein S11
                      30S ribosomal protein S12
                        30S ribosomal protein S13
                          30S ribosomal protein S14
                            30S ribosomal protein S15
                              30S ribosomal protein S16
                                30S ribosomal protein S17
                                  30S ribosomal protein S18
                                    30S ribosomal protein S19
                                      30S ribosomal protein S20
                                        30S ribosomal protein THX
                                          5'-R(*UP*UP*UP*U)-3'nonenonenone
                                          5'-R(*GP*CP*CP*UP*GP*GP*AP*AP*AP*GP*(PSU))-3'nonenonenone
                                          5'-R(P*UP*GP*GP*AP*AP*AP*GP*(PSU))-3'nonenonenone
                                          5'-R(P*UP*UP*U)-3'nonenonenone