Crystal structure of the 30S ribosome in complex with compound 1

Structural Biology Knowledgebase: 4B3M SBKB.org

Experimental Data Snapshot

  • Resolution: 2.9 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.218

wwPDB Validation Full Report


Sequence Display for 4B3M

Classification: RIBOSOME

Total Structure Weight: 796255.13

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 Mutation: H57R
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 132 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 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 88 Thermus thermophilus Gene Name(s): rpsP TTHA1035
30S RIBOSOMAL PROTEIN S17 Q 104 Thermus thermophilus Mutation: E95Q
Gene Name(s): rpsQ TTHA1683
30S RIBOSOMAL PROTEIN S18 R 88 Thermus thermophilus Mutation: A45G
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 Mutation: I34V
Gene Name(s): rpsT rps20 TTHA1397
30S RIBOSOMAL PROTEIN THX V 26 Thermus thermophilus EC#: IUBMB
Gene Name(s): rpsU TTHA1396
Macromolecule Entities
Molecule Chains Length Organism Details
16S RIBOSOMAL RNA A 1521 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*CP)-3' Z 16 Thermus thermophilus

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
Query on ON0

A (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6- diamino-2,6-dideoxy-beta-L-idopyranosyl)- beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2- amino-4,6-O-benzylidene-2-deoxy-alpha-D-glucopyranoside
C30 H49 N5 O14
Ligand Explorer
Binding Pocket (JSmol)
Electron Density (JSmol)
Query on ZN

Ligand Explorer
Binding Pocket (JSmol)
Electron Density (JSmol)
Query on K

Ligand Explorer
Binding Pocket (JSmol)
Electron Density (JSmol)
Query on MG

A, B, D, E, H, I, K, L, M, N, Q, T, Z MAGNESIUM ION
Ligand Explorer
Binding Pocket (JSmol)
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Resolution: 2.9 Å
  • R-Value Free: 0.251
  • R-Value Work: 0.218
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 401.65 α = 90.00
b = 401.65 β = 90.00
c = 175.26 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots

Entry History

Deposition Data

  • Deposited Date: 2012-07-25
  • Released Date: 2013-08-07
  • Deposition author(s): Ng, C.L., Lang, K., Shcherbakov, D., Matt, T., Perez-Fernandez, D., Patak, R., Meyer, M., Duscha, S., Akbergenov, R., Boukari, H., Freihofer, P., Kudyba, I., Reddy, M.S.K., Nandurikar, R.S., Ramakrishnan, V., Vasella, A., Bottger, E.C.

Revision History

  • 2014-02-12
    Type: Citation | Details: JRNL
  • 2014-02-12
    Type: Sequence database correspondence | Details: DBREF
  • 2014-01-29
    Type: Citation | Details: JRNL
  • 2013-11-06
    Type: Entry title | Details: TITLE
  • 2013-11-06
    Type: Other | Details: MASTER, REMARK 900