2HHH

Crystal structure of kasugamycin bound to the 30S ribosomal subunit

Structural Biology Knowledgebase: 2HHH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.265

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2HHH

Classification: RIBOSOME

Total Structure Weight: 784444.07


Macromolecule Entities
Molecule Chains Length Organism Details
30S ribosomal protein S2 B 256 Thermus thermophilus Gene Name(s): rpsB rps2 TTHA0861
30S ribosomal protein S3 C 239 Thermus thermophilus Gene Name(s): rpsC rps3 TTHA1686
30S ribosomal protein S4 D 209 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
30S ribosomal protein S5 E 162 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 156 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 128 Thermus thermophilus Mutation: H58R
Gene Name(s): rpsI rps9 TTHA1464
30S ribosomal protein S10 J 105 Thermus thermophilus Gene Name(s): rpsJ TTHA1693
30S ribosomal protein S11 K 129 Thermus thermophilus Gene Name(s): rpsK rps11 TTHA1666
30S ribosomal protein S12 L 135 Thermus thermophilus Gene Name(s): rpsL TTHA1697
30S ribosomal protein S13 M 126 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
30S ribosomal protein S14 N 61 Thermus thermophilus Gene Name(s): rpsZ rpsN TTHA1679
30S ribosomal protein S15 O 89 Thermus thermophilus Gene Name(s): rpsO TTHA1138
30S ribosomal protein S16 P 88 Thermus thermophilus Gene Name(s): rpsP TTHA1035
30S ribosomal protein S17 Q 105 Thermus thermophilus Gene Name(s): rpsQ TTHA1683
30S ribosomal protein S18 R 88 Thermus thermophilus Gene Name(s): rpsR TTHA0243
30S ribosomal protein S19 S 93 Thermus thermophilus Gene Name(s): rpsS TTHA1688
30S ribosomal protein S20 T 106 Thermus thermophilus Gene Name(s): rpsT rps20 TTHA1397
30S ribosomal protein Thx U 27 Thermus thermophilus EC#: 4.1.1.3 IUBMB
Gene Name(s): rpsU TTHA1396
Macromolecule Entities
Molecule Chains Length Organism Details
16S ribosomal RNA A 1522 Thermus thermophilus

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
KSG
Query on KSG

A (1S,2R,3S,4R,5S,6S)-2,3,4,5,6-PENTAHYDROXYCYCLOHEXYL 2- AMINO-4-{[CARBOXY(IMINO)METHYL]AMINO}-2,3,4,6- TETRADEOXY-ALPHA-D-ARABINO-HEXOPYRANOSIDE
KASUGAMYCIN (Synonym)
C14 H25 N3 O9
PVTHJAPFENJVNC-MHRBZPPQSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.35 Å
  • R-Value Free: 0.289
  • R-Value Work: 0.265
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 410.44 α = 90.00
b = 410.44 β = 90.00
c = 172.65 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-06-28
  • Released Date: 2006-09-26
  • Deposition author(s): Schluenzen, F.

Revision History

  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4