4GKK

Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human mitochondrial anticodon stem loop (ASL) of transfer RNA Methionine (TRNAMET) bound to an mRNA with an AUA-codon in the A-site and paromomycin

Structural Biology Knowledgebase: 4GKK SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.195

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4GKK

Classification: RIBOSOME / ANTIBIOTIC

Total Structure Weight: 777313.32


Macromolecule Entities
Molecule Chains Length Organism Details
30S ribosomal protein S2 B 234 Thermus thermophilus Gene Name(s): rpsB rps2 TTHA0861
30S ribosomal protein S3 C 206 Thermus thermophilus Gene Name(s): rpsC rps3 TTHA1686
30S ribosomal protein S4 D 208 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
30S ribosomal protein S5 E 150 Thermus thermophilus Gene Name(s): rpsE TTHA1675
30S ribosomal protein S6 F 101 Thermus thermophilus Gene Name(s): rpsF TTHA0245
30S ribosomal protein S7 G 155 Thermus thermophilus Gene Name(s): rpsG rps7 TTHA1696
30S ribosomal protein S8 H 138 Thermus thermophilus Gene Name(s): rpsH TTHA1678
30S ribosomal protein S9 I 127 Thermus thermophilus Mutation: H58R
Gene Name(s): rpsI rps9 TTHA1464
30S ribosomal protein S10 J 98 Thermus thermophilus Gene Name(s): rpsJ TTHA1693
30S ribosomal protein S11 K 119 Thermus thermophilus Gene Name(s): rpsK rps11 TTHA1666
30S ribosomal protein S12 L 124 Thermus thermophilus Gene Name(s): rpsL TTHA1697
30S ribosomal protein S13 M 125 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
30S ribosomal protein S14 type Z N 60 Thermus thermophilus Gene Name(s): rpsZ rpsN TTHA1679
30S ribosomal protein S15 O 88 Thermus thermophilus Gene Name(s): rpsO TTHA1138
30S ribosomal protein S16 P 83 Thermus thermophilus Gene Name(s): rpsP TTHA1035
30S ribosomal protein S17 Q 104 Thermus thermophilus Mutation: E96Q
Gene Name(s): rpsQ TTHA1683
30S ribosomal protein S18 R 73 Thermus thermophilus Mutation: A60G
Gene Name(s): rpsR TTHA0243
30S ribosomal protein S19 S 80 Thermus thermophilus Gene Name(s): rpsS TTHA1688
30S ribosomal protein S20 T 99 Thermus thermophilus Mutation: I41V
Gene Name(s): rpsT rps20 TTHA1397
30S ribosomal protein Thx V 24 Thermus thermophilus EC#: 4.1.1.3 IUBMB
Gene Name(s): rpsU TTHA1396
Macromolecule Entities
Molecule Chains Length Organism Details
16S rRNA A 1513 Thermus thermophilus
mRNA A-site fragment W 6 Synthetic construct
tRNA ASL human mitochondrial Met X 17 Synthetic construct

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PAR
Query on PAR

A PAROMOMYCIN
CATENULIN,, AMMINOSIDIN (Synonym)
C23 H45 N5 O14
UOZODPSAJZTQNH-LSWIJEOBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

D, N ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, T MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
PSU
Query on PSU
X RNA LINKING C9 H13 N2 O9 P U
RSQ
Query on RSQ
X RNA LINKING C10 H14 N3 O9 P C

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.195
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 402.37 α = 90.00
b = 402.37 β = 90.00
c = 175.62 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-08-11
  • Released Date: 2013-06-05
  • Deposition author(s): Cantara, W.A., Murphy IV, F.V., Spears, J.L., Demirci, H., Agris, P.F.

Revision History

  • 2013-07-17
    Type: Citation | Details: Citation update
  • 2013-07-03
    Type: Citation | Details: Citation update
  • 2013-06-19
    Type: Citation | Details: Citation update
  • 2013-06-12
    Type: Polymer description | Details: Remove BIRD description