5HL7

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

Structural Biology Knowledgebase: 5HL7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.187

Literature

Macromolecules
Sequence Display for 5HL7

Classification: RIBOSOME

Total Structure Weight: 1365458.00


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 Mutation: G174K
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 SAOUHSC_01784
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 L28 U 62 Staphylococcus aureus Gene Name(s): rpmB SAOUHSC_01191
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 SAOUHSC_01785
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
50S ribosomal protein L36 4 37 Staphylococcus aureus Gene Name(s): rpmJ SAOUHSC_02488
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 7 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
62B
Query on 62B

X Lefamulin
C28 H45 N O5 S
KPVIXBKIJXZQJX-FCEONZPQSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EPE
Query on EPE

N 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, Y 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

J, Q, X, Z (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

A, R, T, X, Y, Z MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EOH
Query on EOH

S, X ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, C, G, I, J, M, O, P, 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: 3.55 Å
  • R-Value Free: 0.227
  • R-Value Work: 0.187
  • Space Group: P 65 2 2

Unit Cell:

Length (Å) Angle (°)
a = 282.11 α = 90.00
b = 282.11 β = 90.00
c = 875.34 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2016-01-14
  • Released Date: 2016-12-21
  • Deposition author(s): Eyal, Z., Matzov, D., Krupkin, M., Rozenberg, H., Zimmerman, E., Bashan, A., Yonath, A.

Revision History

No revisions since initial release