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

Macromolecule Annotations for the Entities in PDB 4DR7

Domain Annotation: CATH CATH Database (version 4.0.0) Homepage

Chains Domain Class Architecture Topology Homology
B1 4dr7B01 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Glucose-6-phosphate isomerase like protein; domain 1
B2 4dr7B02 Mainly Alpha Orthogonal Bundle Helix Hairpins Helix hairpin bin
C1 4dr7C01 Alpha Beta 2-Layer Sandwich GMP Synthetase; Chain A, domain 3
C2 4dr7C02 Alpha Beta 2-Layer Sandwich Ribosomal protein S3 C-terminal domain
D1 4dr7D01 Mainly Alpha Orthogonal Bundle Ribosomal Protein S4 Delta 41; Chain A, domain 1 Ribosomal Protein S4 Delta 41; Chain A, domain 1
D2 4dr7D02 Alpha Beta Roll Structural Genomics Hypothetical 15.5 Kd Protein In mrcA- pckA Intergenic Region; Chain A Structural Genomics Hypothetical 15.5 Kd Protein In Mrca- pcka Intergenic Region; Chain
E1 4dr7E01 Alpha Beta 2-Layer Sandwich Double Stranded RNA Binding Domain
E2 4dr7E02 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5; domain 2
F 4dr7F00 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits
G 4dr7G00 Mainly Alpha Orthogonal Bundle Ribosomal Protein S7 Ribosomal Protein S7;
H2 4dr7H02 Alpha Beta 2-Layer Sandwich Dna Ligase; domain 1
I 4dr7I00 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5; domain 2
K 4dr7K00 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase; domain 5
L 4dr7L00 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
M1 4dr7M01 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein; domain 3
M2 4dr7M02 Few Secondary Structures Irregular 30s ribosomal protein s13; domain 2 30s ribosomal protein s13, domain 2
N 4dr7N00 Few Secondary Structures Irregular 30s Ribosomal Protein S14; Chain N 30s Ribosomal Protein S14; Chain N
O 4dr7O00 Mainly Alpha Orthogonal Bundle Helix Hairpins
R 4dr7R00 Few Secondary Structures Irregular 30s Ribosomal Protein S18 30s Ribosomal Protein S18
S 4dr7S00 Alpha Beta 2-Layer Sandwich 30s Ribosomal Protein S19; Chain A 30s Ribosomal Protein S19; Chain A
T 4dr7T00 Mainly Alpha Up-down Bundle Methane Monooxygenase Hydroxylase; Chain G, domain 1

Protein Family Annotation Pfam Database Homepage

Chains Pfam Accession Pfam Identifier Pfam Description Type Source
R PF01084 Ribosomal_S18 Ribosomal protein S18 Family
Q PF00366 Ribosomal_S17 Ribosomal protein S17 Domain PFAM PF00366
H PF00410 Ribosomal_S8 Ribosomal protein S8 Domain PFAM PF00410
N PF00253 Ribosomal_S14 Ribosomal protein S14p/S29e Family
E PF03719 Ribosomal_S5_C Ribosomal protein S5, C-terminal domain Domain PFAM PF03719
D PF00163 Ribosomal_S4 Ribosomal protein S4/S9 N-terminal domain Family
I PF00380 Ribosomal_S9 Ribosomal protein S9/S16 Family
S PF00203 Ribosomal_S19 Ribosomal protein S19 Domain PFAM PF00203
F PF01250 Ribosomal_S6 Ribosomal protein S6 Domain PFAM PF01250
K PF00411 Ribosomal_S11 Ribosomal protein S11 Family
T PF01649 Ribosomal_S20p Ribosomal protein S20 Family
L PF00164 Ribosom_S12_S23 Ribosomal protein S12/S23 Family
E PF00333 Ribosomal_S5 Ribosomal protein S5, N-terminal domain Domain PFAM PF00333
M PF00416 Ribosomal_S13 Ribosomal protein S13/S18 Family
C PF07650 KH_2 KH domain Domain PFAM PF07650
P PF00886 Ribosomal_S16 Ribosomal protein S16 Family
J PF00338 Ribosomal_S10 Ribosomal protein S10p/S20e Family
B PF00318 Ribosomal_S2 Ribosomal protein S2 Family
D PF01479 S4 S4 domain Domain 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. PFAM PF01479
O PF00312 Ribosomal_S15 Ribosomal protein S15 Domain PFAM PF00312
C PF00189 Ribosomal_S3_C Ribosomal protein S3, C-terminal domain Domain This 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. PFAM PF00189
G PF00177 Ribosomal_S7 Ribosomal protein S7p/S5e Domain This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. PFAM PF00177

Gene Product Annotation Gene Ontology Consortium Homepage

Chains Polymer Molecular Function Biological Process Cellular Component
A 16S rRNA (4DR7:A)
  • none
  • none
  • none
B 30S ribosomal protein S2 (4DR7:B)
C 30S ribosomal protein S3 (4DR7:C)
D 30S ribosomal protein S4 (4DR7:D)
E 30S ribosomal protein S5 (4DR7:E)
F 30S ribosomal protein S6 (4DR7:F)
G 30S ribosomal protein S7 (4DR7:G)
H 30S ribosomal protein S8 (4DR7:H)
I 30S ribosomal protein S9 (4DR7:I)
J 30S ribosomal protein S10 (4DR7:J)
K 30S ribosomal protein S11 (4DR7:K)
L 30S ribosomal protein S12 (4DR7:L)
M 30S ribosomal protein S13 (4DR7:M)
N 30S ribosomal protein S14 (4DR7:N)
O 30S ribosomal protein S15 (4DR7:O)
P 30S ribosomal protein S16 (4DR7:P)
Q 30S ribosomal protein S17 (4DR7:Q)
R 30S ribosomal protein S18 (4DR7:R)
S 30S ribosomal protein S19 (4DR7:S)
T 30S ribosomal protein S20 (4DR7:T)
U 30S ribosomal protein THX (4DR7:U)
  • none
V 5'-R(*UP*UP*UP*U)-3' (4DR7:V)
  • none
  • none
  • none
W 5'-R(*GP*CP*CP*UP*GP*GP*AP*AP*AP*GP*(PSU))- 3' (4DR7:W)
  • none
  • none
  • none
a 5'-R(P*UP*GP*GP*AP*AP*AP*GP*(PSU))-3' (4DR7:a)
  • none
  • none
  • none
b 5'-R(P*UP*UP*U)-3' (4DR7:b)
  • none
  • none
  • none