3OW2

Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.222 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history



Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L2PC [auth A]237Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L3PD [auth B]337Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L4PE [auth C]246Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L5PF [auth D]165Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L6PG [auth E]172Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L7AeH [auth F]119Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10EI [auth G]62Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L10eJ [auth H]167Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for A0A0X1KGB2 (Haloarcula marismortui)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L13PK [auth I]142Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L14PL [auth J]132Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15PM [auth K]150Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L15eN [auth L]194Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for A0A0X1KGB3 (Haloarcula marismortui)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18PO [auth M]186Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L18eP [auth N]115Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L19eQ [auth O]143Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L21eR [auth P]95Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L22PS [auth Q]150Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L23PT [auth R]81Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24PU [auth S]119Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L24eV [auth T]53Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L29PW [auth U]65Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L30PX [auth V]154Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L31eY [auth W]82Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L32eZ [auth X]142Haloarcula 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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37AeAA [auth Y]73Haloarcula marismortuiMutation(s): 0 
UniProt
Find proteins for A0A0X1KGB4 (Haloarcula marismortui)
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L37eBA [auth Z]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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L39eCA [auth 1]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
MoleculeChains Sequence LengthOrganismDetailsImage
50S ribosomal protein L44EDA [auth 2]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
MoleculeChains LengthOrganismImage
23S RIBOSOMAL RNAA [auth 0]2,902Haloarcula marismortui
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Entity ID: 2
MoleculeChains LengthOrganismImage
5S RIBOSOMAL RNAB [auth 9]122Haloarcula marismortui
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Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EMK
Query on EMK

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KG [auth 0](2R,3S,4R,5R,8R,10R,11R,12S,13S,14R)-2-ethyl-3,4,10-trihydroxy-3,5,6,8,10,12,14-heptamethyl-15-oxo-11-[(3,4,6-trideoxy-3-{[3-(1-{(1S,2R)-1-(fluoromethyl)-2-hydroxy-2-[4-(methylsulfonyl)phenyl]ethyl}-1H-1,2,3-triazol-4-yl)propyl](methyl)amino}-beta-D-xylo-hexopyranosyl)oxy]-1-oxa-6-azacyclopentadecan-13-yl 2,6-dideoxy-3-C-methyl-3-O-methyl-alpha-L-ribo-hexopyranoside
C52 H88 F N5 O15 S
YWHOXJJBJDOIMO-BOBSHVDTSA-N
CD
Query on CD

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QH [auth T],
TH [auth Y],
UH [auth Z],
XH [auth 2]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
SR
Query on SR

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AE [auth 0]
AF [auth 0]
AG [auth 0]
AH [auth F]
BE [auth 0]
AE [auth 0],
AF [auth 0],
AG [auth 0],
AH [auth F],
BE [auth 0],
BF [auth 0],
BG [auth 0],
CE [auth 0],
CF [auth 0],
CG [auth 0],
DE [auth 0],
DF [auth 0],
DG [auth 0],
EE [auth 0],
EF [auth 0],
EG [auth 0],
FE [auth 0],
FF [auth 0],
FG [auth 0],
GD [auth 0],
GE [auth 0],
GF [auth 0],
GG [auth 0],
HD [auth 0],
HE [auth 0],
HF [auth 0],
HG [auth 0],
ID [auth 0],
IE [auth 0],
IF [auth 0],
IG [auth 0],
JD [auth 0],
JE [auth 0],
JF [auth 0],
JG [auth 0],
KD [auth 0],
KE [auth 0],
KF [auth 0],
LD [auth 0],
LE [auth 0],
LF [auth 0],
MD [auth 0],
ME [auth 0],
MF [auth 0],
ND [auth 0],
NE [auth 0],
NF [auth 0],
NG [auth 9],
NH [auth Q],
OD [auth 0],
OE [auth 0],
OF [auth 0],
OG [auth 9],
OH [auth R],
PD [auth 0],
PE [auth 0],
PF [auth 0],
PG [auth 9],
QD [auth 0],
QE [auth 0],
QF [auth 0],
RD [auth 0],
RE [auth 0],
RF [auth 0],
RG [auth A],
SD [auth 0],
SE [auth 0],
SF [auth 0],
SG [auth A],
TD [auth 0],
TE [auth 0],
TF [auth 0],
TG [auth A],
UD [auth 0],
UE [auth 0],
UF [auth 0],
UG [auth A],
VD [auth 0],
VE [auth 0],
VF [auth 0],
VH [auth Z],
WD [auth 0],
WE [auth 0],
WF [auth 0],
WG [auth B],
WH [auth Z],
XD [auth 0],
XE [auth 0],
XF [auth 0],
XG [auth B],
YD [auth 0],
YE [auth 0],
YF [auth 0],
YH [auth 2],
ZD [auth 0],
ZE [auth 0],
ZF [auth 0],
ZH [auth 2]
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
K
Query on K

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HC [auth 0]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL
Query on CL

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BD [auth 0]
CD [auth 0]
CH [auth I]
DD [auth 0]
DH [auth I]
BD [auth 0],
CD [auth 0],
CH [auth I],
DD [auth 0],
DH [auth I],
ED [auth 0],
FD [auth 0],
HH [auth L],
IH [auth N],
MH [auth Q],
QG [auth A],
SH [auth X],
ZG [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG
Query on MG

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AB [auth 0]
AC [auth 0]
BB [auth 0]
BC [auth 0]
CB [auth 0]
AB [auth 0],
AC [auth 0],
BB [auth 0],
BC [auth 0],
CB [auth 0],
CC [auth 0],
DB [auth 0],
DC [auth 0],
EA [auth 0],
EB [auth 0],
EC [auth 0],
EH [auth J],
FA [auth 0],
FB [auth 0],
FC [auth 0],
FH [auth K],
GA [auth 0],
GB [auth 0],
GC [auth 0],
HA [auth 0],
HB [auth 0],
IA [auth 0],
IB [auth 0],
JA [auth 0],
JB [auth 0],
KA [auth 0],
KB [auth 0],
LA [auth 0],
LB [auth 0],
LG [auth 9],
MA [auth 0],
MB [auth 0],
NA [auth 0],
NB [auth 0],
OA [auth 0],
OB [auth 0],
PA [auth 0],
PB [auth 0],
PH [auth S],
QA [auth 0],
QB [auth 0],
RA [auth 0],
RB [auth 0],
RH [auth X],
SA [auth 0],
SB [auth 0],
TA [auth 0],
TB [auth 0],
UA [auth 0],
UB [auth 0],
VA [auth 0],
VB [auth 0],
VG [auth B],
WA [auth 0],
WB [auth 0],
XA [auth 0],
XB [auth 0],
YA [auth 0],
YB [auth 0],
ZA [auth 0],
ZB [auth 0]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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AD [auth 0]
BH [auth I]
GH [auth L]
IC [auth 0]
JC [auth 0]
AD [auth 0],
BH [auth I],
GH [auth L],
IC [auth 0],
JC [auth 0],
JH [auth P],
KC [auth 0],
KH [auth Q],
LC [auth 0],
LH [auth Q],
MC [auth 0],
MG [auth 9],
NC [auth 0],
OC [auth 0],
PC [auth 0],
QC [auth 0],
RC [auth 0],
SC [auth 0],
TC [auth 0],
UC [auth 0],
VC [auth 0],
WC [auth 0],
XC [auth 0],
YC [auth 0],
YG [auth C],
ZC [auth 0]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.222 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.853α = 90
b = 298β = 90
c = 574.985γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
MOSFLMdata reduction
SCALAdata scaling
CNXphasing
CNXrefinement

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2012-06-20 
  • Deposition Author(s): Kanyo, Z.F.

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release