2F4V

30S ribosome + designer antibiotic

Structural Biology Knowledgebase: 2F4V SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.8 Å
  • R-Value Free: 0.315
  • R-Value Work: 0.259

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2F4V

Classification: ribosome

Total Structure Weight: 781871.84


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 Mutation: N199Q, Q201N
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 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 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
Macromolecule Entities
Molecule Chains Length Organism Details
16S ribosomal RNA A 1511 Thermus thermophilus
5'-R(P*UP*UP*CP*U)-3' Z 4 Thermus thermophilus

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
AB9
Query on AB9

A (2R)-4-AMINO-N-{(1R,2S,3R,4R,5S)-5-AMINO- 2-{2-[(2-AMINOETHYL)AMINO]ETHOXY}-4-[(2,6- DIAMINO-2,6-DIDEOXY-ALPHA-D-GLUCOPYRANOSYL)OXY]- 3-HYDROXYCYCLOHEXYL}-2-HYDROXYBUTANAMIDE
C20 H43 N7 O8
OGRDTONULPXNRP-HSDDYVLRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
D2C
Query on D2C

A (2S,4S,4AR,5AS,6S,11R,11AS,12R,12AR)-7-CHLORO- 4-(DIMETHYLAMINO)-6,10,11,12-TETRAHYDROXY- 1,3-DIOXO-1,2,3,4,4A,5,5A,6,11,11A,12,12A- DODECAHYDROTETRACENE-2-CARBOXAMIDE
C21 H25 Cl N2 O7
DMSXRSJJYGANOR-VAVXRSHRSA-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 POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, D, M, 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: 3.8 Å
  • R-Value Free: 0.315
  • R-Value Work: 0.259
  • Space Group: P 41 21 2

Unit Cell:

Length (Å) Angle (°)
a = 403.32 α = 90.00
b = 403.32 β = 90.00
c = 176.68 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-11-24
  • Released Date: 2006-07-04
  • Deposition author(s): Murray, J.B., Meroueh, S.O., Russell, R.J., Lentzen, G., Haddad, J., Mobashery, S.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4