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

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

Protein Modification Annotation

Type PDB Residue Nr. Description