5HL7

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A novel pleuromutilin antibacterial compound, its binding mode and selectivity mechanism.

Eyal, Z.Matzov, D.Krupkin, M.Paukner, S.Riedl, R.Rozenberg, H.Zimmerman, E.Bashan, A.Yonath, A.

(2016) Sci Rep 6: 39004-39004

  • DOI: https://doi.org/10.1038/srep39004
  • Primary Citation of Related Structures:  
    5HL7

  • PubMed Abstract: 

    The increasing appearance of pathogenic bacteria with antibiotic resistance is a global threat. Consequently, clinically available potent antibiotics that are active against multidrug resistant pathogens are becoming exceedingly scarce. Ribosomes are a main target for antibiotics, and hence are an objective for novel drug development. Lefamulin, a semi-synthetic pleuromutilin compound highly active against multi-resistant pathogens, is a promising antibiotic currently in phase III trials for the treatment of community-acquired bacterial pneumonia in adults. The crystal structure of the Staphylococcus aureus large ribosomal subunit in complex with lefamulin reveals its protein synthesis inhibition mechanism and the rationale for its potency. In addition, analysis of the bacterial and eukaryotes ribosome structures around the pleuromutilin binding pocket has elucidated the key for the drug's selectivity.


  • Organizational Affiliation

    Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2277Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth B]220Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth C]207Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth D]179Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth E]178Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13H [auth G]145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14I [auth H]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15J [auth I]140Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L16K [auth J]144Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L17L [auth K]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18M [auth L]119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19N [auth M]116Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L20O [auth N]118Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21P [auth O]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22Q [auth P]117Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23R [auth Q]91Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24S [auth R]105Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L25T [auth S]217Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L27U [auth T]94Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L28V [auth U]62Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29W [auth V]69Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30X [auth W]59Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32Y [auth Z]58Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L34Z [auth 2]45Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L35AA [auth 3]66Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L36BA [auth 4]37Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains LengthOrganismImage
23S ribosomal RNAB [auth X]2,923Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 3
MoleculeChains LengthOrganismImage
5S ribosomal RNAC [auth Y]114Staphylococcus aureus subsp. aureus NCTC 8325
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
62B
Query on 62B

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IA [auth X]Lefamulin
C28 H45 N O5 S
KPVIXBKIJXZQJX-FCEONZPQSA-N
EPE
Query on EPE

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LU [auth N]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
SPD
Query on SPD

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CU [auth Y]
DT [auth X]
ET [auth X]
FT [auth X]
GT [auth X]
CU [auth Y],
DT [auth X],
ET [auth X],
FT [auth X],
GT [auth X],
HT [auth X],
IT [auth X],
JT [auth X]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
MPD
Query on MPD

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IU [auth J]
JA [auth X]
KA [auth X]
LA [auth X]
MA [auth X]
IU [auth J],
JA [auth X],
KA [auth X],
LA [auth X],
MA [auth X],
NA [auth X],
OA [auth X],
OU [auth Q],
PA [auth X],
QA [auth X],
SU [auth Z]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MN
Query on MN

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AB [auth X]
AC [auth X]
AD [auth X]
AE [auth X]
AF [auth X]
AB [auth X],
AC [auth X],
AD [auth X],
AE [auth X],
AF [auth X],
AG [auth X],
AH [auth X],
AI [auth X],
AR [auth X],
AS [auth X],
BB [auth X],
BC [auth X],
BD [auth X],
BE [auth X],
BF [auth X],
BG [auth X],
BH [auth X],
BO [auth X],
BS [auth X],
CA [auth A],
CB [auth X],
CC [auth X],
CD [auth X],
CE [auth X],
CF [auth X],
CG [auth X],
CH [auth X],
CJ [auth X],
CK [auth X],
CR [auth X],
CS [auth X],
DB [auth X],
DC [auth X],
DD [auth X],
DE [auth X],
DF [auth X],
DG [auth X],
DI [auth X],
DS [auth X],
EB [auth X],
EC [auth X],
ED [auth X],
EE [auth X],
EG [auth X],
EH [auth X],
EM [auth X],
ES [auth X],
FB [auth X],
FC [auth X],
FD [auth X],
FE [auth X],
FG [auth X],
FH [auth X],
FI [auth X],
FJ [auth X],
FM [auth X],
FS [auth X],
GA [auth X],
GB [auth X],
GC [auth X],
GD [auth X],
GE [auth X],
GF [auth X],
GG [auth X],
GH [auth X],
GI [auth X],
GJ [auth X],
GM [auth X],
GS [auth X],
HB [auth X],
HC [auth X],
HD [auth X],
HE [auth X],
HF [auth X],
HG [auth X],
HH [auth X],
HI [auth X],
HK [auth X],
HM [auth X],
HP [auth X],
HQ [auth X],
HS [auth X],
IB [auth X],
IC [auth X],
ID [auth X],
IE [auth X],
IF [auth X],
IG [auth X],
IH [auth X],
II [auth X],
IJ [auth X],
IK [auth X],
IM [auth X],
IS [auth X],
JB [auth X],
JC [auth X],
JD [auth X],
JE [auth X],
JF [auth X],
JG [auth X],
JH [auth X],
JK [auth X],
JM [auth X],
JR [auth X],
JS [auth X],
KB [auth X],
KC [auth X],
KD [auth X],
KE [auth X],
KF [auth X],
KG [auth X],
KH [auth X],
KM [auth X],
KQ [auth X],
KR [auth X],
LB [auth X],
LC [auth X],
LD [auth X],
LE [auth X],
LF [auth X],
LG [auth X],
LH [auth X],
LM [auth X],
LQ [auth X],
MB [auth X],
MC [auth X],
MD [auth X],
ME [auth X],
MG [auth X],
MH [auth X],
MI [auth X],
MM [auth X],
NB [auth X],
NC [auth X],
ND [auth X],
NE [auth X],
NG [auth X],
NH [auth X],
NI [auth X],
NM [auth X],
NT [auth X],
OB [auth X],
OC [auth X],
OE [auth X],
OF [auth X],
OH [auth X],
OI [auth X],
OJ [auth X],
OM [auth X],
OQ [auth X],
OT [auth X],
PB [auth X],
PC [auth X],
PD [auth X],
PE [auth X],
PF [auth X],
PG [auth X],
PH [auth X],
PK [auth X],
PM [auth X],
PO [auth X],
PR [auth X],
PS [auth X],
PU [auth R],
QB [auth X],
QC [auth X],
QD [auth X],
QE [auth X],
QH [auth X],
QI [auth X],
QJ [auth X],
QM [auth X],
QP [auth X],
QR [auth X],
QS [auth X],
RA [auth X],
RB [auth X],
RC [auth X],
RD [auth X],
RE [auth X],
RG [auth X],
RH [auth X],
RI [auth X],
RM [auth X],
RO [auth X],
RP [auth X],
RR [auth X],
RS [auth X],
RT [auth Y],
RU [auth T],
SA [auth X],
SB [auth X],
SC [auth X],
SD [auth X],
SE [auth X],
SG [auth X],
SH [auth X],
SM [auth X],
SP [auth X],
SR [auth X],
TA [auth X],
TB [auth X],
TC [auth X],
TD [auth X],
TE [auth X],
TG [auth X],
TM [auth X],
TP [auth X],
TR [auth X],
TU [auth Z],
UA [auth X],
UB [auth X],
UC [auth X],
UD [auth X],
UE [auth X],
UF [auth X],
UG [auth X],
UH [auth X],
UI [auth X],
UO [auth X],
UP [auth X],
UR [auth X],
VA [auth X],
VB [auth X],
VC [auth X],
VD [auth X],
VE [auth X],
VF [auth X],
VG [auth X],
VH [auth X],
VO [auth X],
VR [auth X],
WA [auth X],
WB [auth X],
WC [auth X],
WD [auth X],
WE [auth X],
WF [auth X],
WG [auth X],
WH [auth X],
WI [auth X],
WJ [auth X],
WP [auth X],
WR [auth X],
XA [auth X],
XB [auth X],
XC [auth X],
XD [auth X],
XE [auth X],
XF [auth X],
XG [auth X],
XH [auth X],
XM [auth X],
XR [auth X],
XT [auth Y],
YA [auth X],
YB [auth X],
YC [auth X],
YD [auth X],
YF [auth X],
YG [auth X],
YH [auth X],
YP [auth X],
YR [auth X],
ZA [auth X],
ZB [auth X],
ZC [auth X],
ZD [auth X],
ZE [auth X],
ZF [auth X],
ZG [auth X],
ZH [auth X],
ZQ [auth X],
ZR [auth X]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
EOH
Query on EOH

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KT [auth X],
LT [auth X],
QU [auth S]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
MG
Query on MG

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AJ [auth X]
AK [auth X]
AL [auth X]
AM [auth X]
AN [auth X]
AJ [auth X],
AK [auth X],
AL [auth X],
AM [auth X],
AN [auth X],
AO [auth X],
AP [auth X],
AQ [auth X],
AT [auth X],
AU [auth Y],
BI [auth X],
BJ [auth X],
BK [auth X],
BL [auth X],
BM [auth X],
BN [auth X],
BP [auth X],
BQ [auth X],
BR [auth X],
BT [auth X],
BU [auth Y],
CI [auth X],
CL [auth X],
CM [auth X],
CN [auth X],
CO [auth X],
CP [auth X],
CQ [auth X],
CT [auth X],
DA [auth A],
DH [auth X],
DJ [auth X],
DK [auth X],
DL [auth X],
DM [auth X],
DN [auth X],
DO [auth X],
DP [auth X],
DQ [auth X],
DR [auth X],
DU [auth C],
EA [auth A],
EF [auth X],
EI [auth X],
EJ [auth X],
EK [auth X],
EL [auth X],
EN [auth X],
EO [auth X],
EP [auth X],
EQ [auth X],
ER [auth X],
EU [auth C],
FA [auth A],
FF [auth X],
FK [auth X],
FL [auth X],
FN [auth X],
FO [auth X],
FP [auth X],
FQ [auth X],
FR [auth X],
FU [auth G],
GK [auth X],
GL [auth X],
GN [auth X],
GO [auth X],
GP [auth X],
GQ [auth X],
GR [auth X],
GU [auth G],
HA [auth X],
HJ [auth X],
HL [auth X],
HN [auth X],
HO [auth X],
HR [auth X],
HU [auth I],
IL [auth X],
IN [auth X],
IO [auth X],
IP [auth X],
IQ [auth X],
IR [auth X],
JI [auth X],
JJ [auth X],
JL [auth X],
JN [auth X],
JO [auth X],
JP [auth X],
JQ [auth X],
JU [auth J],
KI [auth X],
KJ [auth X],
KK [auth X],
KL [auth X],
KN [auth X],
KO [auth X],
KP [auth X],
KS [auth X],
KU [auth M],
LI [auth X],
LJ [auth X],
LK [auth X],
LL [auth X],
LN [auth X],
LO [auth X],
LP [auth X],
LR [auth X],
LS [auth X],
MF [auth X],
MJ [auth X],
MK [auth X],
ML [auth X],
MN [auth X],
MO [auth X],
MP [auth X],
MQ [auth X],
MR [auth X],
MS [auth X],
MT [auth X],
MU [auth O],
NF [auth X],
NJ [auth X],
NK [auth X],
NL [auth X],
NN [auth X],
NO [auth X],
NP [auth X],
NQ [auth X],
NR [auth X],
NS [auth X],
NU [auth P],
OD [auth X],
OG [auth X],
OK [auth X],
OL [auth X],
ON [auth X],
OO [auth X],
OP [auth X],
OR [auth X],
OS [auth X],
PI [auth X],
PJ [auth X],
PL [auth X],
PN [auth X],
PP [auth X],
PQ [auth X],
PT [auth X],
QF [auth X],
QG [auth X],
QK [auth X],
QL [auth X],
QN [auth X],
QO [auth X],
QQ [auth X],
QT [auth Y],
RF [auth X],
RJ [auth X],
RK [auth X],
RL [auth X],
RN [auth X],
RQ [auth X],
SF [auth X],
SI [auth X],
SJ [auth X],
SK [auth X],
SL [auth X],
SN [auth X],
SO [auth X],
SQ [auth X],
SS [auth X],
ST [auth Y],
TF [auth X],
TH [auth X],
TI [auth X],
TJ [auth X],
TK [auth X],
TL [auth X],
TN [auth X],
TO [auth X],
TQ [auth X],
TS [auth X],
TT [auth Y],
UJ [auth X],
UK [auth X],
UL [auth X],
UM [auth X],
UN [auth X],
UQ [auth X],
US [auth X],
UT [auth Y],
VI [auth X],
VJ [auth X],
VK [auth X],
VL [auth X],
VM [auth X],
VN [auth X],
VP [auth X],
VQ [auth X],
VS [auth X],
VT [auth Y],
WK [auth X],
WL [auth X],
WM [auth X],
WN [auth X],
WO [auth X],
WQ [auth X],
WS [auth X],
WT [auth Y],
XI [auth X],
XJ [auth X],
XK [auth X],
XL [auth X],
XN [auth X],
XO [auth X],
XP [auth X],
XQ [auth X],
XS [auth X],
YE [auth X],
YI [auth X],
YJ [auth X],
YK [auth X],
YL [auth X],
YM [auth X],
YN [auth X],
YO [auth X],
YQ [auth X],
YS [auth X],
YT [auth Y],
ZI [auth X],
ZJ [auth X],
ZK [auth X],
ZL [auth X],
ZM [auth X],
ZN [auth X],
ZO [auth X],
ZP [auth X],
ZS [auth X],
ZT [auth Y]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.55 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.189 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 282.112α = 90
b = 282.112β = 90
c = 875.343γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description