4KHP

Structure of the Thermus thermophilus 30S ribosomal subunit in complex with de-6-MSA-pactamycin

Structural Biology Knowledgebase: 4KHP SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.185

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4KHP

Classification: RIBOSOME / ANTIBIOTIC

Total Structure Weight: 770164.06


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 125 Thermus thermophilus Gene Name(s): rpsL TTHA1697
30S Ribosomal protein S13 M 120 Thermus thermophilus Gene Name(s): rpsM rps13 TTHA1667
30S Ribosomal protein S14 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 99 Thermus thermophilus Gene Name(s): rpsQ TTHA1683
30S Ribosomal protein S18 R 70 Thermus thermophilus Gene Name(s): rpsR TTHA0243
30S Ribosomal protein S19 S 78 Thermus thermophilus Gene Name(s): rpsS TTHA1688
30S Ribosomal protein S20 T 99 Thermus thermophilus Gene Name(s): rpsT rps20 TTHA1397
30S Ribosomal protein THX U 24 Thermus thermophilus EC#: 4.1.1.3 IUBMB
Gene Name(s): rpsU TTHA1396
Macromolecule Entities
Molecule Chains Length Organism Details
16S Ribosomal RNA A 1506 Thermus thermophilus
Fragment of messenger RNA X 6 Thermus thermophilus

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)
PCY
Query on PCY

A Pactamycin
C28 H38 N4 O8
WVIUOSJLUCTGFK-JUJPXXQGSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, D, E, K, S MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.226
  • R-Value Work: 0.185
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 401.00 α = 90.00
b = 401.00 β = 90.00
c = 176.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-05-01
  • Released Date: 2013-06-05
  • Deposition author(s): Tourigny, D.S., Fernandez, I.S., Kelley, A.C., Ramakrishnan, V.

Revision History

  • 2013-10-30
    Type: Citation | Details: Citation update