5HKV

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.66 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural insights of lincosamides targeting the ribosome of Staphylococcus aureus.

Matzov, D.Eyal, Z.Benhamou, R.I.Shalev-Benami, M.Halfon, Y.Krupkin, M.Zimmerman, E.Rozenberg, H.Bashan, A.Fridman, M.Yonath, A.

(2017) Nucleic Acids Res 45: 10284-10292

  • DOI: 10.1093/nar/gkx658
  • Primary Citation of Related Structures:  
    5HKV, 5NRG

  • PubMed Abstract: 
  • Antimicrobial resistance within a wide range of pathogenic bacteria is an increasingly serious threat to global public health. Among these pathogenic bacteria are the highly resistant, versatile and possibly aggressive bacteria, Staphylococcus aureus. Lincosamide antibiotics were proved to be effective against this pathogen ...

    Antimicrobial resistance within a wide range of pathogenic bacteria is an increasingly serious threat to global public health. Among these pathogenic bacteria are the highly resistant, versatile and possibly aggressive bacteria, Staphylococcus aureus. Lincosamide antibiotics were proved to be effective against this pathogen. This small, albeit important group of antibiotics is mostly active against Gram-positive bacteria, but also used against selected Gram-negative anaerobes and protozoa. S. aureus resistance to lincosamides can be acquired by modifications and/or mutations in the rRNA and rProteins. Here, we present the crystal structures of the large ribosomal subunit of S. aureus in complex with the lincosamides lincomycin and RB02, a novel semisynthetic derivative and discuss the biochemical aspects of the in vitro potency of various lincosamides. These results allow better understanding of the drugs selectivity as well as the importance of the various chemical moieties of the drug for binding and inhibition.


    Organizational Affiliation

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



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L2C [auth A]277Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplBSAOUHSC_02509
UniProt
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3D [auth B]220Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplCSAOUHSC_02512
UniProt
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L4E [auth C]207Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplDSAOUHSC_02511
UniProt
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L5F [auth D]179Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplESAOUHSC_02500
UniProt
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L6G [auth E]178Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplFSAOUHSC_02496
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L13H [auth G]145Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplMSAOUHSC_02478
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L14I [auth H]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplNSAOUHSC_02502
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L15J [auth I]146Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplOSAOUHSC_02492
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L16K [auth J]144Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplPSAOUHSC_02505
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L17L [auth K]122Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplQSAOUHSC_02484
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L18M [auth L]119Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplRSAOUHSC_02495
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L19N [auth M]116Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplSSAOUHSC_01211
UniProt
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L20O [auth N]118Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplTSAOUHSC_01784
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21P [auth O]102Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplUSAOUHSC_01757
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L22Q [auth P]117Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplVSAOUHSC_02507
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L23R [auth Q]91Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplWSAOUHSC_02510
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L24S [auth R]105Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplXSAOUHSC_02501
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L25T [auth S]217Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rplYctcSAOUHSC_00474
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L27U [auth T]94Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmASAOUHSC_01755
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L28V [auth U]62Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmBSAOUHSC_01191
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L29W [auth V]69Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmCSAOUHSC_02504
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L30X [auth W]59Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmDSAOUHSC_02493
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L32Y [auth Z]58Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmFSAOUHSC_01078
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L34Z [auth 2]45Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmHSAOUHSC_03055
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L35AA [auth 3]66Staphylococcus aureus subsp. aureus NCTC 8325Mutation(s): 0 
Gene Names: rpmISAOUHSC_01785
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23s ribosomal RNAA [auth X]2923Staphylococcus aureus subsp. aureus NCTC 8325
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S ribosomal RNAB [auth Y]114Staphylococcus aureus subsp. aureus NCTC 8325
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Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3QB (Subject of Investigation/LOI)
Query on 3QB

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BA [auth X]LINCOMYCIN
C18 H34 N2 O6 S
OJMMVQQUTAEWLP-KIDUDLJLSA-N
 Ligand Interaction
SPD
Query on SPD

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OS [auth X] , PS [auth X] , QS [auth X] , RS [auth X] , RT [auth Y] , SS [auth X] , TS [auth X] , US [auth X] , 
OS [auth X], PS [auth X], QS [auth X], RS [auth X], RT [auth Y], SS [auth X], TS [auth X], US [auth X], VS [auth X]
SPERMIDINE
C7 H19 N3
ATHGHQPFGPMSJY-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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CA [auth X] , DA [auth X] , EA [auth X] , FA [auth X] , GA [auth X] , HA [auth X] , IA [auth X] , JA [auth X] , 
CA [auth X], DA [auth X], EA [auth X], FA [auth X], GA [auth X], HA [auth X], IA [auth X], JA [auth X], KA [auth X], LA [auth X], MA [auth X], NA [auth X], OA [auth X], PA [auth X], QA [auth X], RA [auth X], RU [auth S], SA [auth X], TA [auth X], UA [auth X], VA [auth X], WA [auth X], XA [auth X], YA [auth X]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
MN
Query on MN

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AB [auth X] , AC [auth X] , AF [auth X] , AH [auth X] , AI [auth X] , AJ [auth X] , AK [auth X] , AL [auth X] , 
AB [auth X], AC [auth X], AF [auth X], AH [auth X], AI [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], AR [auth X], BB [auth X], BC [auth X], BH [auth X], BI [auth X], BJ [auth X], BK [auth X], BL [auth X], BM [auth X], BN [auth X], BO [auth X], BP [auth X], BQ [auth X], BR [auth X], CB [auth X], CC [auth X], CH [auth X], CI [auth X], CJ [auth X], CK [auth X], CL [auth X], CM [auth X], CN [auth X], CO [auth X], CP [auth X], CQ [auth X], CR [auth X], DB [auth X], DC [auth X], DG [auth X], DH [auth X], DI [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], DT [auth X], EB [auth X], EC [auth X], EG [auth X], EH [auth X], EI [auth X], EJ [auth X], EK [auth X], EL [auth X], EM [auth X], EN [auth X], EO [auth X], EP [auth X], EQ [auth X], ET [auth X], EU [auth I], FB [auth X], FG [auth X], FH [auth X], FI [auth X], FJ [auth X], FK [auth X], FL [auth X], FM [auth X], FN [auth X], FO [auth X], FP [auth X], FQ [auth X], FT [auth Y], FU [auth J], GB [auth X], GF [auth X], GH [auth X], GI [auth X], GJ [auth X], GK [auth X], GL [auth X], GM [auth X], GN [auth X], GO [auth X], GP [auth X], GQ [auth X], GT [auth Y], GU [auth J], HE [auth X], HF [auth X], HH [auth X], HI [auth X], HJ [auth X], HK [auth X], HL [auth X], HM [auth X], HN [auth X], HO [auth X], HP [auth X], HQ [auth X], ID [auth X], IE [auth X], IF [auth X], IH [auth X], II [auth X], IJ [auth X], IK [auth X], IL [auth X], IM [auth X], IN [auth X], IO [auth X], IP [auth X], IQ [auth X], JD [auth X], JE [auth X], JH [auth X], JI [auth X], JJ [auth X], JK [auth X], JL [auth X], JM [auth X], JN [auth X], JO [auth X], JP [auth X], JQ [auth X], KD [auth X], KE [auth X], KH [auth X], KI [auth X], KJ [auth X], KK [auth X], KL [auth X], KM [auth X], KN [auth X], KO [auth X], KP [auth X], KQ [auth X], KU [auth N], LE [auth X], LH [auth X], LI [auth X], LJ [auth X], LK [auth X], LL [auth X], LM [auth X], LN [auth X], LO [auth X], LP [auth X], LQ [auth X], LT [auth Y], ME [auth X], MH [auth X], MI [auth X], MJ [auth X], MK [auth X], ML [auth X], MM [auth X], MN [auth X], MO [auth X], MP [auth X], MQ [auth X], MT [auth Y], NE [auth X], NG [auth X], NH [auth X], NI [auth X], NJ [auth X], NK [auth X], NL [auth X], NM [auth X], NN [auth X], NO [auth X], NP [auth X], NQ [auth X], NT [auth Y], OE [auth X], OG [auth X], OH [auth X], OI [auth X], OJ [auth X], OK [auth X], OL [auth X], OM [auth X], ON [auth X], OO [auth X], OP [auth X], OQ [auth X], OT [auth Y], PE [auth X], PH [auth X], PI [auth X], PJ [auth X], PK [auth X], PL [auth X], PM [auth X], PN [auth X], PO [auth X], PP [auth X], PQ [auth X], PT [auth Y], PU [auth R], QE [auth X], QG [auth X], QH [auth X], QI [auth X], QJ [auth X], QK [auth X], QL [auth X], QM [auth X], QN [auth X], QO [auth X], QP [auth X], QQ [auth X], QT [auth Y], RE [auth X], RG [auth X], RH [auth X], RI [auth X], RJ [auth X], RK [auth X], RL [auth X], RM [auth X], RN [auth X], RO [auth X], RP [auth X], RQ [auth X], SE [auth X], SG [auth X], SH [auth X], SI [auth X], SJ [auth X], SK [auth X], SL [auth X], SM [auth X], SN [auth X], SO [auth X], SP [auth X], SQ [auth X], ST [auth A], TE [auth X], TG [auth X], TH [auth X], TI [auth X], TJ [auth X], TK [auth X], TL [auth X], TM [auth X], TN [auth X], TO [auth X], TP [auth X], TQ [auth X], TU [auth S], UE [auth X], UG [auth X], UH [auth X], UI [auth X], UJ [auth X], UK [auth X], UL [auth X], UM [auth X], UN [auth X], UO [auth X], UP [auth X], UQ [auth X], VE [auth X], VG [auth X], VH [auth X], VI [auth X], VJ [auth X], VK [auth X], VL [auth X], VM [auth X], VN [auth X], VO [auth X], VP [auth X], VQ [auth X], VT [auth A], VU [auth Z], WE [auth X], WG [auth X], WH [auth X], WI [auth X], WJ [auth X], WK [auth X], WL [auth X], WM [auth X], WN [auth X], WO [auth X], WP [auth X], WQ [auth X], XE [auth X], XG [auth X], XH [auth X], XI [auth X], XJ [auth X], XK [auth X], XL [auth X], XM [auth X], XN [auth X], XO [auth X], XP [auth X], XQ [auth X], YE [auth X], YG [auth X], YH [auth X], YI [auth X], YJ [auth X], YK [auth X], YL [auth X], YM [auth X], YN [auth X], YO [auth X], YP [auth X], YQ [auth X], YT [auth C], ZA [auth X], ZE [auth X], ZG [auth X], ZH [auth X], ZI [auth X], ZJ [auth X], ZK [auth X], ZL [auth X], ZM [auth X], ZN [auth X], ZO [auth X], ZP [auth X], ZQ [auth X], ZT [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
EOH
Query on EOH

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AT [auth X] , AU [auth C] , BT [auth X] , CT [auth X] , QU [auth R] , WS [auth X] , XS [auth X] , YS [auth X] , 
AT [auth X], AU [auth C], BT [auth X], CT [auth X], QU [auth R], WS [auth X], XS [auth X], YS [auth X], ZS [auth X]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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HT [auth Y]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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AD [auth X] , AE [auth X] , AG [auth X] , AS [auth X] , BD [auth X] , BE [auth X] , BF [auth X] , BG [auth X] , 
AD [auth X], AE [auth X], AG [auth X], AS [auth X], BD [auth X], BE [auth X], BF [auth X], BG [auth X], BS [auth X], BU [auth G], CD [auth X], CE [auth X], CF [auth X], CG [auth X], CS [auth X], CU [auth G], DD [auth X], DE [auth X], DF [auth X], DR [auth X], DS [auth X], DU [auth G], ED [auth X], EE [auth X], EF [auth X], ER [auth X], ES [auth X], FC [auth X], FD [auth X], FE [auth X], FF [auth X], FR [auth X], FS [auth X], GC [auth X], GD [auth X], GE [auth X], GG [auth X], GR [auth X], GS [auth X], HB [auth X], HC [auth X], HD [auth X], HG [auth X], HR [auth X], HS [auth X], HU [auth K], IB [auth X], IC [auth X], IG [auth X], IR [auth X], IS [auth X], IT [auth Y], IU [auth L], JB [auth X], JC [auth X], JF [auth X], JG [auth X], JR [auth X], JS [auth X], JT [auth Y], JU [auth M], KB [auth X], KC [auth X], KF [auth X], KG [auth X], KR [auth X], KS [auth X], KT [auth Y], LB [auth X], LC [auth X], LD [auth X], LF [auth X], LG [auth X], LR [auth X], LS [auth X], LU [auth O], MB [auth X], MC [auth X], MD [auth X], MF [auth X], MG [auth X], MR [auth X], MS [auth X], MU [auth P], NB [auth X], NC [auth X], ND [auth X], NF [auth X], NR [auth X], NS [auth X], NU [auth P], OB [auth X], OC [auth X], OD [auth X], OF [auth X], OR [auth X], OU [auth R], PB [auth X], PC [auth X], PD [auth X], PF [auth X], PG [auth X], PR [auth X], QB [auth X], QC [auth X], QD [auth X], QF [auth X], QR [auth X], RB [auth X], RC [auth X], RD [auth X], RF [auth X], RR [auth X], SB [auth X], SC [auth X], SD [auth X], SF [auth X], SR [auth X], SU [auth S], TB [auth X], TC [auth X], TD [auth X], TF [auth X], TR [auth X], TT [auth A], UB [auth X], UC [auth X], UD [auth X], UF [auth X], UR [auth X], UT [auth A], UU [auth T], VB [auth X], VC [auth X], VD [auth X], VF [auth X], VR [auth X], WB [auth X], WC [auth X], WD [auth X], WF [auth X], WR [auth X], WT [auth A], WU [auth 2], XB [auth X], XC [auth X], XD [auth X], XF [auth X], XR [auth X], XT [auth B], XU [auth 3], YB [auth X], YC [auth X], YD [auth X], YF [auth X], YR [auth X], YU [auth 3], ZB [auth X], ZC [auth X], ZD [auth X], ZF [auth X], ZR [auth X]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.66 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.190 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 280.885α = 90
b = 280.885β = 90
c = 873.522γ = 120
Software Package:
Software NamePurpose
HKL-2000data reduction
XSCALEdata 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: 2017-05-03
    Type: Initial release
  • Version 1.1: 2017-05-10
    Changes: Database references, Structure summary
  • Version 1.2: 2017-08-09
    Changes: Database references
  • Version 1.3: 2017-10-11
    Changes: Database references