1SM1

COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN

Structural Biology Knowledgebase: 1SM1 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 0.348
  • R-Value Work: 0.278

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1SM1

Classification: RIBOSOME / ANTIBIOTIC

Total Structure Weight: 1390063.38


Macromolecule Entities
Molecule Chains Length Organism Details
50S RIBOSOMAL PROTEIN L33 1 82 Deinococcus radiodurans Gene Name(s): rpmG DR_2049
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L34 2 47 Deinococcus radiodurans Gene Name(s): rpmH DR_2152
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L35 3 66 Deinococcus radiodurans Gene Name(s): rpmI DR_2005
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L36 4 37 Deinococcus radiodurans Gene Name(s): rpmJ DR_2124
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
QUINUPRISTIN 5 8 Streptomyces graminofaciens
50S RIBOSOMAL PROTEIN L2 A 275 Deinococcus radiodurans Gene Name(s): rplB DR_0314
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L3 B 211 Deinococcus radiodurans Gene Name(s): rplC DR_0311
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L4 C 205 Deinococcus radiodurans Gene Name(s): rplD DR_0312
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L5 D 180 Deinococcus radiodurans Gene Name(s): rplE DR_0323
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L6 E 212 Deinococcus radiodurans Gene Name(s): rplF DR_2111
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L9 F 146 Deinococcus radiodurans Gene Name(s): rplI DR_0102
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L11 G 144 Deinococcus radiodurans Gene Name(s): rplK DR_2046
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L13 H 174 Deinococcus radiodurans Gene Name(s): rplM DR_0174
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L14 I 134 Deinococcus radiodurans Gene Name(s): rplN DR_0321
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L15 J 156 Deinococcus radiodurans Gene Name(s): rplO DR_2115
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L16 K 142 Deinococcus radiodurans Gene Name(s): rplP DR_0318
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L17 L 116 Deinococcus radiodurans Gene Name(s): rplQ DR_2129
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L18 M 114 Deinococcus radiodurans Gene Name(s): rplR DR_2112
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L19 N 166 Deinococcus radiodurans Gene Name(s): rplS DR_0755
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L20 O 118 Deinococcus radiodurans Gene Name(s): rplT DR_2004
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L21 P 100 Deinococcus radiodurans Gene Name(s): rplU DR_0086
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L22 Q 134 Deinococcus radiodurans Gene Name(s): rplV DR_0316
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L23 R 95 Deinococcus radiodurans Gene Name(s): rplW DR_0313
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L24 S 115 Deinococcus radiodurans Gene Name(s): rplX DR_0322
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
GENERAL STRESS PROTEIN CTC T 253 Deinococcus radiodurans Gene Name(s): rplY ctc DR_0427
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L27 U 91 Deinococcus radiodurans Gene Name(s): rpmA DR_0085
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L29 W 67 Deinococcus radiodurans Gene Name(s): rpmC DR_0319
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L30 X 55 Deinococcus radiodurans Gene Name(s): rpmD DR_2114
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L31 Y 73 Deinococcus radiodurans Gene Name(s): rpmE DR_0825
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S RIBOSOMAL PROTEIN L32 Z 60 Deinococcus radiodurans Gene Name(s): rpmF DR_2366
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
23S RIBOSOMAL RNA 0 2880 Deinococcus radiodurans
5S RIBOSOMAL RNA 9 124 Deinococcus radiodurans

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DOL
Query on DOL

0 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY- 10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28- TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)- PENTAENE-2,8,14,23-TETRAONE
DALFOPRISTIN (Synonym)
C34 H50 N4 O9 S
SUYRLXYYZQTJHF-VMBLUXKRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000505 (DBB,THR,004,MHW,PRO,MHU,MHV,MHT) 5 Quinupristin Oligopeptide /
Antibiotic
Ligand Explorer

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.42 Å
  • R-Value Free: 0.348
  • R-Value Work: 0.278
  • Space Group: I 2 2 2

Unit Cell:

Length (Å) Angle (°)
a = 168.50 α = 90.00
b = 406.00 β = 90.00
c = 693.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-03-08
  • Released Date: 2004-08-03
  • Deposition author(s): Harms, J.M., Schluenzen, F., Fucini, P., Bartels, H., Yonath, A.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-27
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-27
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-27
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-27
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-27
    Type: Linkage | Details: Linkage
  • 2011-07-27
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-27
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4