1HNX

STRUCTURE OF THE THERMUS THERMOPHILUS 30S RIBOSOMAL SUBUNIT IN COMPLEX WITH PACTAMYCIN

Structural Biology Knowledgebase: 1HNX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.232

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1HNX

Classification: RIBOSOME

Total Structure Weight: 788352.89


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 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 V 26 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
FRAGMENT OF MESSENGER RNA X 6 Thermus thermophilus

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

A Pactamycin
C28 H38 N4 O8
WVIUOSJLUCTGFK-JUJPXXQGSA-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, D, H MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.232
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 401.72 α = 90.00
b = 401.72 β = 90.00
c = 177.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2000-12-08
  • Released Date: 2001-02-21
  • Deposition author(s): Brodersen, D.E., Clemons Jr., W.M., Carter, A.P., Morgan-Warren, R., Wimberly, B.T., Ramakrishnan, V.

Revision History

  • 2013-05-22
    Type: Non-polymer description | Details: The name of ligand PCY was corrected
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4