3OW2

Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.221

Literature

Macromolecules
Sequence Display for 3OW2

Classification: RIBOSOME

Total Structure Weight: 1410134.38


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L2P A 237 Haloarcula marismortui Gene Name(s): rpl2 rrnAC1608
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3P B 337 Haloarcula marismortui Gene Name(s): rpl3 rrnAC1611
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4P C 246 Haloarcula marismortui Gene Name(s): rpl4 rrnAC1610
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5P D 165 Haloarcula marismortui Gene Name(s): rpl5 rrnAC1598
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6P E 172 Haloarcula marismortui Gene Name(s): rpl6 rrnAC1596
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L7Ae F 119 Haloarcula marismortui Gene Name(s): rpl7ae rrnAC0103
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L10E G 62 Haloarcula marismortui Gene Name(s): rpl10 rpl10e rplP0 rrnAC1417
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L10e H 167 Haloarcula marismortui Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13P I 142 Haloarcula marismortui Gene Name(s): rpl13 rrnAC0065
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14P J 132 Haloarcula marismortui Gene Name(s): rpl14 rrnAC1602
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15P K 150 Haloarcula marismortui Gene Name(s): rpl15 rrnAC1590
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15e L 194 Haloarcula marismortui Gene Name(s): rpl15e
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18P M 186 Haloarcula marismortui Gene Name(s): rpl18 rrnAC1593
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18e N 115 Haloarcula marismortui Gene Name(s): rpl18e rrnAC0064
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19e O 143 Haloarcula marismortui Mutation: Y71K
Gene Name(s): rpl19e rrnAC1594
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21e P 95 Haloarcula marismortui Gene Name(s): rpl21e rrnAC0260
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22P Q 150 Haloarcula marismortui Gene Name(s): rpl22 rrnAC1606
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23P R 81 Haloarcula marismortui Gene Name(s): rpl23p rrnAC1609
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24P S 119 Haloarcula marismortui Gene Name(s): rpl24p rrnAC1601
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24e T 53 Haloarcula marismortui Gene Name(s): rpl24e rrnAC0104
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29P U 65 Haloarcula marismortui Gene Name(s): rpl29p rrnAC1604
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30P V 154 Haloarcula marismortui Gene Name(s): rpl30p rrnAC1591
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L31e W 82 Haloarcula marismortui Gene Name(s): rpl31e rrnAC3113
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32e X 142 Haloarcula marismortui Gene Name(s): rpl32e rrnAC1595
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L37Ae Y 73 Haloarcula marismortui Gene Name(s): rpl37ae
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L37e Z 56 Haloarcula marismortui Gene Name(s): rpl37e rrnAC0797.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L39e 1 48 Haloarcula marismortui Gene Name(s): rpl39e rrnAC3112
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L44E 2 92 Haloarcula marismortui Gene Name(s): rpl44e rrnAC3514
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
23S RIBOSOMAL RNA 0 2902 Haloarcula marismortui
5S RIBOSOMAL RNA 9 122 Haloarcula marismortui

Small Molecules
Ligands 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EMK
Query on EMK

0 (2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-2-ethyl- 3,4,10-trihydroxy-3,5,6,8,10,12,14-heptamethyl- 15-oxo-11-[(3,4,6-trideoxy-3-{[3-(1-{(1S,2R)- 1-(fluoromethyl)-2-hydroxy-2-[4-(methylsulfonyl)phenyl]ethyl}- 1H-1,2,3-triazol-4-yl)propyl](methyl)amino}- beta-D-xylo-hexopyranosyl)oxy]-1-oxa-6-azacyclopentadecan- 13-yl 2,6-dideoxy-3-C-methyl-3-O-methyl-alpha- L-ribo-hexopyranoside
C52 H88 F N5 O15 S
YWHOXJJBJDOIMO-BOBSHVDTSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CD
Query on CD

2, T, Y, Z CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SR
Query on SR

0, 2, 9, A, B, F, Q, R, Z STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
K
Query on K

0 POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

0, A, D, I, L, N, Q, X CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

0, 9, B, J, K, S, X MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NA
Query on NA

0, 9, C, I, L, P, Q SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.253
  • R-Value Work: 0.221
  • Space Group: C 2 2 21

Unit Cell:

Length (Å) Angle (°)
a = 211.85 α = 90.00
b = 298.00 β = 90.00
c = 574.98 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2010-09-17
  • Released Date: 2012-06-20
  • Deposition author(s): Kanyo, Z.F.

Revision History

  • Version 1_0: 2012-06-20

    Type: Initial release