3OW2

Crystal Structure of Enhanced Macrolide Bound to 50S Ribosomal Subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 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

Literature

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2P
A
237Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl2
Find proteins for P20276 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P20276
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3P
B
337Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl3
Find proteins for P20279 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P20279
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4P
C
246Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl4
Find proteins for P12735 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12735
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5P
D
165Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl5
Find proteins for P14124 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14124
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6P
E
172Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl6
Find proteins for P14135 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14135
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7Ae
F
119Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl7ae
Find proteins for P12743 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12743
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10E
G
62Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl10 (rpl10e, rplP0)
Find proteins for P15825 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P15825
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L10e
H
167Haloarcula marismortuiMutation(s): 0 
Find proteins for A0A0X1KGB2 (Haloarcula marismortui)
Go to UniProtKB:  A0A0X1KGB2
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13P
I
142Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl13
Find proteins for P29198 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P29198
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14P
J
132Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl14
Find proteins for P22450 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P22450
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15P
K
150Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl15
Find proteins for P12737 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12737
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15e
L
194Haloarcula marismortuiMutation(s): 0 
Gene Names: rpl15e
Find proteins for A0A0X1KGB3 (Haloarcula marismortui)
Go to UniProtKB:  A0A0X1KGB3
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18P
M
186Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl18
Find proteins for P14123 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14123
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18e
N
115Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl18e
Find proteins for P12733 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12733
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19e
O
143Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl19e
Find proteins for P14119 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14119
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21e
P
95Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl21e
Find proteins for P12734 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12734
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22P
Q
150Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl22
Find proteins for P10970 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10970
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23P
R
81Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl23
Find proteins for P12732 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12732
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24P
S
119Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl24
Find proteins for P10972 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10972
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24e
T
53Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl24e
Find proteins for P14116 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14116
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29P
U
65Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl29
Find proteins for P10971 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P10971
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30P
V
154Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl30
Find proteins for P14121 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P14121
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31e
W
82Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl31e
Find proteins for P18138 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P18138
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32e
X
142Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl32e
Find proteins for P12736 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P12736
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37Ae
Y
73Haloarcula marismortuiMutation(s): 0 
Gene Names: rpl37ae
Find proteins for A0A0X1KGB4 (Haloarcula marismortui)
Go to UniProtKB:  A0A0X1KGB4
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L37e
Z
56Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl37e
Find proteins for P32410 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P32410
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L39e
1
48Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl39e
Find proteins for P22452 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P22452
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L44E
2
92Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809)Mutation(s): 0 
Gene Names: rpl44e
Find proteins for P32411 (Haloarcula marismortui (strain ATCC 43049 / DSM 3752 / JCM 8966 / VKM B-1809))
Go to UniProtKB:  P32411
Entity ID: 1
MoleculeChainsLengthOrganism
23S RIBOSOMAL RNA02902Haloarcula marismortui
Entity ID: 2
MoleculeChainsLengthOrganism
5S RIBOSOMAL RNA9122Haloarcula marismortui
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
0
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
0, 9, C, I, L, P, Q
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
EMK
Query on EMK

Download SDF File 
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
CL
Query on CL

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

Download SDF File 
Download CCD File 
0, 9, B, J, K, S, X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
SR
Query on SR

Download SDF File 
Download CCD File 
0, 2, 9, A, B, F, Q, R, Z
STRONTIUM ION
Sr
PWYYWQHXAPXYMF-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
2, T, Y, Z
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 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 = 90.00
b = 298.000β = 90.00
c = 574.985γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
CNXrefinement
SCALAdata scaling
MOSFLMdata reduction
CNXphasing
CNSrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



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