4AQY

Structure of ribosome-apramycin complexes

Structural Biology Knowledgebase: 4AQY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.193

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4AQY

Classification: RIBOSOME

Total Structure Weight: 797515.76


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 208 Thermus thermophilus Gene Name(s): rpsD rps4 TTHA1665
30S RIBOSOMAL PROTEIN S5 E 161 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 128 Thermus thermophilus Gene Name(s): rpsI rps9 TTHA1464
30S RIBOSOMAL PROTEIN S10 J 104 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 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 88 Thermus thermophilus Gene Name(s): rpsP TTHA1035
30S RIBOSOMAL PROTEIN S17 Q 104 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 92 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
5'-R(*UP*UP*CP*AP*AP*AP)-3' W 6 Thermus thermophilus
5'-R(*GP*GP*GP*AP*UP*UP*GP*AP*AP*AP*AP*UP*CP*CP*C)-3' Z 15 Thermus thermophilus

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AM2
Query on AM2

A APRAMYCIN
3, (Synonym)
C21 H41 N5 O11
XZNUGFQTQHRASN-XQENGBIVSA-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)
K
Query on K

A, V POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, D, F, G, H, J, K, L, M, S, W, Z MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.5 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.193
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 402.18 α = 90.00
b = 402.18 β = 90.00
c = 175.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-04-20
  • Released Date: 2012-07-18
  • Deposition author(s): Matt, T., Ng, C.L., Lang, K., Sha, S.H., Akbergenov, R., Shcherbakov, D., Meyer, M., Duscha, S., Xie, J., Dubbaka, S.R., Perez-Fernandez, D., Vasella, A., Ramakrishnan, V., Schacht, J., Bottger, E.C.

Revision History

  • 2014-10-08
    Type: Entry title | Details: TITLE