1IBL

STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH A MESSENGER RNA FRAGMENT AND COGNATE TRANSFER RNA ANTICODON STEM-LOOP BOUND AT THE A SITE AND WITH THE ANTIBIOTIC PAROMOMYCIN


Macromolecule Annotations for the Entities in PDB 1IBL

Domain Annotation: SCOP Classification SCOP Database (version: 1.75) Homepage

Chains Domain Info Class Fold Superfamily Family Domain Species
B d1iblb_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
C d1iblc_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
D d1ibld_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
E d1ible_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
F d1iblf_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
G d1iblg_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
H d1iblh_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
I d1ibli_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
J d1iblj_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
K d1iblk_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
L d1ibll_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
M d1iblm_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
N d1ibln_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
O d1iblo_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
P d1iblp_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
Q d1iblq_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
R d1iblr_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
S d1ibls_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
T d1iblt_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]
V d1iblv_ Low resolution protein structures Ribosome and ribosomal fragments Ribosome and ribosomal fragments Ribosome complexes 70S ribosome functional complex Thermus thermophilus [TaxId: 274]

Domain Annotation: CATH CATH Database (version 4.0.0) Homepage

Chains Domain Class Architecture Topology Homology
B2 1iblB02 Mainly Alpha Orthogonal Bundle Helix Hairpins Helix hairpin bin
C1 1iblC01 Alpha Beta 2-Layer Sandwich GMP Synthetase; Chain A, domain 3
C2 1iblC02 Alpha Beta 2-Layer Sandwich Ribosomal protein S3 C-terminal domain
D1 1iblD01 Mainly Alpha Orthogonal Bundle Ribosomal Protein S4 Delta 41; Chain A, domain 1 Ribosomal Protein S4 Delta 41; Chain A, domain 1
D2 1iblD02 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 1iblE01 Alpha Beta 2-Layer Sandwich Double Stranded RNA Binding Domain
E2 1iblE02 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5; domain 2
F 1iblF00 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits
G 1iblG00 Mainly Alpha Orthogonal Bundle Ribosomal Protein S7 Ribosomal Protein S7;
H1 1iblH01 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8; Chain: A, domain 1
H2 1iblH02 Alpha Beta 2-Layer Sandwich Dna Ligase; domain 1
I 1iblI00 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5; domain 2
J 1iblJ00 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits
K 1iblK00 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase; domain 5
L 1iblL00 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
M1 1iblM01 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein; domain 3
M2 1iblM02 Few Secondary Structures Irregular 30s ribosomal protein s13; domain 2 30s ribosomal protein s13, domain 2
N 1iblN00 Few Secondary Structures Irregular 30s Ribosomal Protein S14; Chain N 30s Ribosomal Protein S14; Chain N
O 1iblO00 Mainly Alpha Orthogonal Bundle Helix Hairpins
P 1iblP00 Alpha Beta 2-Layer Sandwich S16 Ribosomal Protein; Chain: A;
Q 1iblQ00 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
R 1iblR00 Few Secondary Structures Irregular 30s Ribosomal Protein S18 30s Ribosomal Protein S18
S 1iblS00 Alpha Beta 2-Layer Sandwich 30s Ribosomal Protein S19; Chain A 30s Ribosomal Protein S19; Chain A
T 1iblT00 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
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
N PF00253 Ribosomal_S14 Ribosomal protein S14p/S29e Family
L PF00164 Ribosom_S12_S23 Ribosomal protein S12/S23 Family
O PF00312 Ribosomal_S15 Ribosomal protein S15 Domain PFAM PF00312
D PF00163 Ribosomal_S4 Ribosomal protein S4/S9 N-terminal domain Family
P PF00886 Ribosomal_S16 Ribosomal protein S16 Family
R PF01084 Ribosomal_S18 Ribosomal protein S18 Family
J PF00338 Ribosomal_S10 Ribosomal protein S10p/S20e Family
E PF00333 Ribosomal_S5 Ribosomal protein S5, N-terminal domain Domain PFAM PF00333
I PF00380 Ribosomal_S9 Ribosomal protein S9/S16 Family
G PF00177 Ribosomal_S7 Ribosomal protein S7p/S5e Domain This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. PFAM PF00177
T PF01649 Ribosomal_S20p Ribosomal protein S20 Family
S PF00203 Ribosomal_S19 Ribosomal protein S19 Domain PFAM PF00203
F PF01250 Ribosomal_S6 Ribosomal protein S6 Domain PFAM PF01250
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
B PF00318 Ribosomal_S2 Ribosomal protein S2 Family
M PF00416 Ribosomal_S13 Ribosomal protein S13/S18 Family
K PF00411 Ribosomal_S11 Ribosomal protein S11 Family
H PF00410 Ribosomal_S8 Ribosomal protein S8 Domain PFAM PF00410
Q PF00366 Ribosomal_S17 Ribosomal protein S17 Domain PFAM PF00366
E PF03719 Ribosomal_S5_C Ribosomal protein S5, C-terminal domain Domain PFAM PF03719
C PF07650 KH_2 KH domain Domain PFAM PF07650

Gene Product Annotation Gene Ontology Consortium Homepage

Chains Polymer Molecular Function Biological Process Cellular Component
A 16S RIBOSOMAL RNA (1IBL:A)
  • none
  • none
  • none
X P-SITE MESSENGER RNA FRAGMENT (1IBL:X)
  • none
  • none
  • none
Y ANTICODON STEM-LOOP OF PHENYLALANINE TRANSFER RNA (1IBL:Y)
  • none
  • none
  • none
Z A-SITE MESSENGER RNA FRAGMENT (1IBL:Z)
  • none
  • none
  • none
B 30S RIBOSOMAL PROTEIN S2 (1IBL:B)
C 30S RIBOSOMAL PROTEIN S3 (1IBL:C)
D 30S RIBOSOMAL PROTEIN S4 (1IBL:D)
E 30S RIBOSOMAL PROTEIN S5 (1IBL:E)
F 30S RIBOSOMAL PROTEIN S6 (1IBL:F)
G 30S RIBOSOMAL PROTEIN S7 (1IBL:G)
H 30S RIBOSOMAL PROTEIN S8 (1IBL:H)
I 30S RIBOSOMAL PROTEIN S9 (1IBL:I)
J 30S RIBOSOMAL PROTEIN S10 (1IBL:J)
K 30S RIBOSOMAL PROTEIN S11 (1IBL:K)
L 30S RIBOSOMAL PROTEIN S12 (1IBL:L)
M 30S RIBOSOMAL PROTEIN S13 (1IBL:M)
N 30S RIBOSOMAL PROTEIN S14 (1IBL:N)
O 30S RIBOSOMAL PROTEIN S15 (1IBL:O)
P 30S RIBOSOMAL PROTEIN S16 (1IBL:P)
Q 30S RIBOSOMAL PROTEIN S17 (1IBL:Q)
R 30S RIBOSOMAL PROTEIN S18 (1IBL:R)
S 30S RIBOSOMAL PROTEIN S19 (1IBL:S)
T 30S RIBOSOMAL PROTEIN S20 (1IBL:T)
V 30S RIBOSOMAL PROTEIN THX (1IBL:V)
  • none

Protein Modification Annotation

Type PDB Residue Nr. Description