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




Macromolecules

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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10eH167Haloarcula marismortuiMutation(s): 0 
Find proteins for A0A0X1KGB2 (Haloarcula marismortui)
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13PI142Haloarcula marismortuiMutation(s): 0 
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P29198
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14PJ132Haloarcula marismortuiMutation(s): 0 
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P22450
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15PK150Haloarcula marismortuiMutation(s): 0 
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15eL194Haloarcula marismortuiMutation(s): 0 
Gene Names: rpl15e
Find proteins for A0A0X1KGB3 (Haloarcula marismortui)
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18PM186Haloarcula marismortuiMutation(s): 0 
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18eN115Haloarcula marismortuiMutation(s): 0 
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P12733
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19eO143Haloarcula marismortuiMutation(s): 0 
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P14119
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21eP95Haloarcula marismortuiMutation(s): 0 
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P12734
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22PQ150Haloarcula marismortuiMutation(s): 0 
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23PR81Haloarcula marismortuiMutation(s): 0 
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P12732
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24PS119Haloarcula marismortuiMutation(s): 0 
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24eT53Haloarcula marismortuiMutation(s): 0 
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P14116
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29PU65Haloarcula marismortuiMutation(s): 0 
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P10971
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30PV154Haloarcula marismortuiMutation(s): 0 
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31eW82Haloarcula marismortuiMutation(s): 0 
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32eX142Haloarcula marismortuiMutation(s): 0 
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37AeY73Haloarcula marismortuiMutation(s): 0 
Gene Names: rpl37ae
Find proteins for A0A0X1KGB4 (Haloarcula marismortui)
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Go to UniProtKB:  A0A0X1KGB4
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37eZ56Haloarcula marismortuiMutation(s): 0 
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L39e148Haloarcula marismortuiMutation(s): 0 
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P22452
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2PA237Haloarcula marismortuiMutation(s): 0 
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P20276
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L44E292Haloarcula marismortuiMutation(s): 0 
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P32411
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3PB337Haloarcula marismortuiMutation(s): 0 
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P20279
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4PC246Haloarcula marismortuiMutation(s): 0 
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12735 
Go to UniProtKB:  P12735
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5PD165Haloarcula marismortuiMutation(s): 0 
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P14124
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6PE172Haloarcula marismortuiMutation(s): 0 
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
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Go to UniProtKB:  P14135
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7AeF119Haloarcula marismortuiMutation(s): 0 
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P12743 
Go to UniProtKB:  P12743
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10EG62Haloarcula marismortuiMutation(s): 0 
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Explore P15825 
Go to UniProtKB:  P15825
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNA02902Haloarcula marismortui

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Entity ID: 2
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNA9122Haloarcula marismortui
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EMK
Query on EMK

Download CCD File 
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
 Ligand Interaction
CD
Query on CD

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2, T, Y, Z
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

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0, 2, 9, A, B, F, Q, R, Z
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

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0
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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0, A, D, I, L, N, Q, X
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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0, 9, B, J, K, S, X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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0, 9, C, I, L, P, Q
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
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

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-09-17 
  • Released Date: 2012-06-20 
  • Deposition Author(s): Kanyo, Z.F.

Revision History 

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