5NRG

The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex with RB02


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.44 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.219

Literature

Macromolecules
Sequence Display for 5NRG

Classification: RIBOSOME

Total Structure Weight: 1344440.75


Macromolecule Entities
Molecule Chains Length Organism Details
50S ribosomal protein L2 A 277 Staphylococcus aureus Gene Name(s): rplB SAOUHSC_02509
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L3 B 220 Staphylococcus aureus Gene Name(s): rplC SAOUHSC_02512
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L4 C 207 Staphylococcus aureus Gene Name(s): rplD SAOUHSC_02511
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L5 D 179 Staphylococcus aureus Gene Name(s): rplE SAOUHSC_02500
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L6 E 178 Staphylococcus aureus Gene Name(s): rplF SAOUHSC_02496
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L13 G 145 Staphylococcus aureus Gene Name(s): rplM SAOUHSC_02478
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L14 H 122 Staphylococcus aureus Gene Name(s): rplN SAOUHSC_02502
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L15 I 140 Staphylococcus aureus Gene Name(s): rplO SAOUHSC_02492
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L16 J 144 Staphylococcus aureus Gene Name(s): rplP SAOUHSC_02505
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L17 K 122 Staphylococcus aureus Gene Name(s): rplQ SAOUHSC_02484
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L18 L 119 Staphylococcus aureus Gene Name(s): rplR SAOUHSC_02495
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L19 M 116 Staphylococcus aureus Gene Name(s): rplS SAOUHSC_01211
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L20 N 118 Staphylococcus aureus Gene Name(s): rplT SAHV_1665
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L21 O 102 Staphylococcus aureus Gene Name(s): rplU SAOUHSC_01757
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L22 P 117 Staphylococcus aureus Gene Name(s): rplV SAOUHSC_02507
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L23 Q 91 Staphylococcus aureus Gene Name(s): rplW SAOUHSC_02510
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L24 R 105 Staphylococcus aureus Gene Name(s): rplX SAOUHSC_02501
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L25 S 217 Staphylococcus aureus Gene Name(s): rplY ctc SAOUHSC_00474
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L27 T 94 Staphylococcus aureus Gene Name(s): rpmA SAOUHSC_01755
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L29 V 69 Staphylococcus aureus Gene Name(s): rpmC SAOUHSC_02504
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L30 W 59 Staphylococcus aureus Gene Name(s): rpmD SAOUHSC_02493
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L32 Z 58 Staphylococcus aureus Gene Name(s): rpmF SAOUHSC_01078
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L34 2 45 Staphylococcus aureus Gene Name(s): rpmH SAOUHSC_03055
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L35 3 66 Staphylococcus aureus Gene Name(s): rpmI SAHV_1666
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Macromolecule Entities
Molecule Chains Length Organism Details
23S ribosomal RNA X 2923 Staphylococcus aureus
5S ribosomal RNA Y 114 Staphylococcus aureus

Small Molecules
Ligands 6 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
95H
Query on 95H

X ~{N}-[(1~{R},2~{R})-1-[(2~{R},3~{R},4~{S},5~{R},6~{R})- 6-methylsulfanyl-3,4,5-tris(oxidanyl)oxan- 2-yl]-2-oxidanyl-propyl]-4-nitro-benzamide
RB02 (Synonym)
C16 H22 N2 O8 S
KAMQPAUJKUPLQE-CVTPPLIDSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EPE
Query on EPE

X 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES (Synonym)
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SPD
Query on SPD

X SPERMIDINE
N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE; PA(34) (Synonym)
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPD
Query on MPD

X (4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

3, E, I, X, Y, Z MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

3, C, G, J, X, Y MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.44 Å
  • R-Value Free: 0.261
  • R-Value Work: 0.219
  • Space Group: P 65 2 2

Unit Cell:

Length (Å) Angle (°)
a = 279.80 α = 90.00
b = 279.80 β = 90.00
c = 873.27 γ = 120.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2017-04-23
  • Released Date: 2017-08-09
  • Deposition author(s): Yonath, A., Matzov, D., Eyal, Z., Ben Hamou, R., Zimmerman, E., Rozenberg, H., Bashan, A., Fridman, M.

Revision History

No revisions since initial release