1KD1

Co-crystal Structure of Spiramycin bound to the 50S Ribosomal Subunit of Haloarcula marismortui


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

The structures of four macrolide antibiotics bound to the large ribosomal subunit.

Hansen, J.L.Ippolito, J.A.Ban, N.Nissen, P.Moore, P.B.Steitz, T.A.

(2002) Mol Cell 10: 117-128

  • DOI: 10.1016/s1097-2765(02)00570-1
  • Primary Citation of Related Structures:  
    1K8A, 1K9M, 1KD1, 1M1K

  • PubMed Abstract: 
  • Crystal structures of the Haloarcula marismortui large ribosomal subunit complexed with the 16-membered macrolide antibiotics carbomycin A, spiramycin, and tylosin and a 15-membered macrolide, azithromycin, show that they bind in the polypeptide exit tunnel adjacent to the peptidyl transferase center ...

    Crystal structures of the Haloarcula marismortui large ribosomal subunit complexed with the 16-membered macrolide antibiotics carbomycin A, spiramycin, and tylosin and a 15-membered macrolide, azithromycin, show that they bind in the polypeptide exit tunnel adjacent to the peptidyl transferase center. Their location suggests that they inhibit protein synthesis by blocking the egress of nascent polypeptides. The saccharide branch attached to C5 of the lactone rings extends toward the peptidyl transferase center, and the isobutyrate extension of the carbomycin A disaccharide overlaps the A-site. Unexpectedly, a reversible covalent bond forms between the ethylaldehyde substituent at the C6 position of the 16-membered macrolides and the N6 of A2103 (A2062, E. coli). Mutations in 23S rRNA that result in clinical resistance render the binding site less complementary to macrolides.


    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, New Haven, Connecticut 06520, USA.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L2C239Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L3D337Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L4E246Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L5F176Haloarcula marismortuiMutation(s): 0 
UniProt
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Entity ID: 7
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RIBOSOMAL PROTEIN L6G177Haloarcula marismortuiMutation(s): 0 
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Entity ID: 8
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RIBOSOMAL PROTEIN L7AEH119Haloarcula marismortuiMutation(s): 0 
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Entity ID: 9
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RIBOSOMAL PROTEIN L10I348Haloarcula marismortuiMutation(s): 0 
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Entity ID: 10
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RIBOSOMAL PROTEIN L10EJ167Haloarcula marismortuiMutation(s): 0 
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Entity ID: 11
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RIBOSOMAL PROTEIN L13K145Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 12
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RIBOSOMAL PROTEIN L14L132Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 13
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RIBOSOMAL PROTEIN L15M164Haloarcula marismortuiMutation(s): 0 
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Entity ID: 14
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RIBOSOMAL PROTEIN L15EN194Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60618 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 15
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RIBOSOMAL PROTEIN L18O186Haloarcula marismortuiMutation(s): 0 
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Entity ID: 16
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RIBOSOMAL PROTEIN L18EP115Haloarcula marismortuiMutation(s): 0 
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Entity ID: 17
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RIBOSOMAL PROTEIN L19EQ148Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 18
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RIBOSOMAL PROTEIN L21ER95Haloarcula marismortuiMutation(s): 0 
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Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 19
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RIBOSOMAL PROTEIN L22S154Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
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RIBOSOMAL PROTEIN L23T84Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 21
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RIBOSOMAL PROTEIN L24U119Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 22
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RIBOSOMAL PROTEIN L24EV66Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L29W70Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L30X154Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L31EY91Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L32EZ240Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37AeAA [auth 1]73Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P60619 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L37EBA [auth 2]56Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L39ECA [auth 3]48Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
RIBOSOMAL PROTEIN L44EDA [auth 4]92Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S RRNAA 2922Haloarcula marismortui
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S RRNAB 122Haloarcula marismortui
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Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SPR
Query on SPR

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EA [auth A]SPIRAMYCIN I
C43 H74 N2 O14
ACTOXUHEUCPTEW-CEUOBAOPSA-N
 Ligand Interaction
CD
Query on CD

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AJ [auth 1],
BJ [auth 2],
DJ [auth 4],
NI [auth P],
WI [auth V]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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RH [auth A],
SH [auth A],
TH [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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AI [auth D],
EI [auth K],
EJ [auth 4],
FI [auth K],
GI [auth K],
AI [auth D],
EI [auth K],
EJ [auth 4],
FI [auth K],
GI [auth K],
IH [auth A],
JH [auth A],
JI [auth M],
KH [auth A],
LH [auth A],
LI [auth N],
MH [auth A],
MI [auth O],
NH [auth A],
OH [auth A],
OI [auth P],
PH [auth A],
QH [auth A],
QI [auth R],
TI [auth S],
YI [auth Z],
ZH [auth C]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
BB [auth A],
AB [auth A],
AC [auth A],
AD [auth A],
AE [auth A],
BB [auth A],
BC [auth A],
BD [auth A],
BE [auth A],
CB [auth A],
CC [auth A],
CD [auth A],
CE [auth A],
CJ [auth 4],
DB [auth A],
DC [auth A],
DD [auth A],
DE [auth A],
EB [auth A],
EC [auth A],
ED [auth A],
EE [auth A],
FA [auth A],
FB [auth A],
FC [auth A],
FD [auth A],
FE [auth A],
GA [auth A],
GB [auth A],
GC [auth A],
GD [auth A],
GE [auth A],
HA [auth A],
HB [auth A],
HC [auth A],
HD [auth A],
HE [auth A],
HI [auth L],
IA [auth A],
IB [auth A],
IC [auth A],
ID [auth A],
IE [auth A],
JA [auth A],
JB [auth A],
JC [auth A],
JD [auth A],
JE [auth A],
KA [auth A],
KB [auth A],
KC [auth A],
KD [auth A],
KE [auth A],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth A],
LE [auth A],
MA [auth A],
MB [auth A],
MC [auth A],
MD [auth A],
ME [auth A],
NA [auth A],
NB [auth A],
NC [auth A],
ND [auth A],
OA [auth A],
OB [auth A],
OC [auth A],
OD [auth A],
PA [auth A],
PB [auth A],
PC [auth A],
PD [auth A],
QA [auth A],
QB [auth A],
QC [auth A],
QD [auth A],
RA [auth A],
RB [auth A],
RC [auth A],
RD [auth A],
SA [auth A],
SB [auth A],
SC [auth A],
SD [auth A],
TA [auth A],
TB [auth A],
TC [auth A],
TD [auth A],
UA [auth A],
UB [auth A],
UC [auth A],
UD [auth A],
UH [auth B],
VA [auth A],
VB [auth A],
VC [auth A],
VD [auth A],
VI [auth U],
WA [auth A],
WB [auth A],
WC [auth A],
WD [auth A],
XA [auth A],
XB [auth A],
XC [auth A],
XD [auth A],
XH [auth C],
XI [auth Z],
YA [auth A],
YB [auth A],
YC [auth A],
YD [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth A],
ZD [auth A],
ZI [auth 1]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
AF [auth A],
AG [auth A],
AH [auth A],
BF [auth A],
BG [auth A],
AF [auth A],
AG [auth A],
AH [auth A],
BF [auth A],
BG [auth A],
BH [auth A],
BI [auth E],
CF [auth A],
CG [auth A],
CH [auth A],
CI [auth J],
DF [auth A],
DG [auth A],
DH [auth A],
DI [auth K],
EF [auth A],
EG [auth A],
EH [auth A],
FF [auth A],
FG [auth A],
FH [auth A],
GF [auth A],
GG [auth A],
GH [auth A],
HF [auth A],
HG [auth A],
HH [auth A],
IF [auth A],
IG [auth A],
II [auth M],
JF [auth A],
JG [auth A],
KF [auth A],
KG [auth A],
KI [auth N],
LF [auth A],
LG [auth A],
MF [auth A],
MG [auth A],
NE [auth A],
NF [auth A],
NG [auth A],
OE [auth A],
OF [auth A],
OG [auth A],
PE [auth A],
PF [auth A],
PG [auth A],
PI [auth R],
QE [auth A],
QF [auth A],
QG [auth A],
RE [auth A],
RF [auth A],
RG [auth A],
RI [auth S],
SE [auth A],
SF [auth A],
SG [auth A],
SI [auth S],
TE [auth A],
TF [auth A],
TG [auth A],
UE [auth A],
UF [auth A],
UG [auth A],
UI [auth T],
VE [auth A],
VF [auth A],
VG [auth A],
VH [auth B],
WE [auth A],
WF [auth A],
WG [auth A],
WH [auth B],
XE [auth A],
XF [auth A],
XG [auth A],
YE [auth A],
YF [auth A],
YG [auth A],
YH [auth C],
ZE [auth A],
ZF [auth A],
ZG [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.220 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.902α = 90
b = 300.474β = 90
c = 575.176γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-19
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance