6DDD

Structure of the 50S ribosomal subunit from Methicillin Resistant Staphylococcus aureus in complex with the oxazolidinone antibiotic LZD-5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

cryoEM-Guided Development of Antibiotics for Drug-Resistant Bacteria.

Belousoff, M.J.Venugopal, H.Wright, A.Seoner, S.Stuart, I.Stubenrauch, C.Bamert, R.S.Lupton, D.W.Lithgow, T.

(2019) ChemMedChem 14: 527-531


Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
A
116Staphylococcus aureusMutation(s): 0 
Gene Names: rplS (rplS_1, rplS_2)
Find proteins for A0A077UVB6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UVB6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
B
276Staphylococcus aureusMutation(s): 0 
Gene Names: rap (rplB)
Find proteins for B3VKN3 (Staphylococcus aureus)
Go to UniProtKB:  B3VKN3
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L20
C
118Staphylococcus aureusMutation(s): 0 
Gene Names: rplT (rplT_2)
Find proteins for A0A077VMP6 (Staphylococcus aureus)
Go to UniProtKB:  A0A077VMP6
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
D
102Staphylococcus aureusMutation(s): 0 
Gene Names: rplU (rplU_1)
Find proteins for D7URR3 (Staphylococcus aureus)
Go to UniProtKB:  D7URR3
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
E
116Staphylococcus aureusMutation(s): 0 
Gene Names: rplV (rplV_1)
Find proteins for A0A077UKF9 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UKF9
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
F
91Staphylococcus aureusMutation(s): 0 
Gene Names: rplW (rplW_1)
Find proteins for W8TUB4 (Staphylococcus aureus)
Go to UniProtKB:  W8TUB4
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
G
105Staphylococcus aureusMutation(s): 0 
Gene Names: rplX (rplX_1)
Find proteins for W8TRD5 (Staphylococcus aureus)
Go to UniProtKB:  W8TRD5
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
H
217Staphylococcus aureusMutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for A0A133Q8Z9 (Staphylococcus aureus)
Go to UniProtKB:  A0A133Q8Z9
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
I
85Staphylococcus aureusMutation(s): 0 
Gene Names: rpmA (rpmA_1, rpmA_2)
Find proteins for A0A077ULC5 (Staphylococcus aureus)
Go to UniProtKB:  A0A077ULC5
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
J
62Staphylococcus aureusMutation(s): 0 
Gene Names: rpmB (rpmB_1)
Find proteins for A0A077URJ8 (Staphylococcus aureus)
Go to UniProtKB:  A0A077URJ8
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
K
69Staphylococcus aureusMutation(s): 0 
Gene Names: rpmC (rpmC_1)
Find proteins for A0A077W1J5 (Staphylococcus aureus)
Go to UniProtKB:  A0A077W1J5
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
L
217Staphylococcus aureusMutation(s): 0 
Gene Names: rplC (rplC_1)
Find proteins for W8U3W0 (Staphylococcus aureus)
Go to UniProtKB:  W8U3W0
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
M
59Staphylococcus aureusMutation(s): 0 
Gene Names: rpmD (rpmD_1)
Find proteins for W8UVN7 (Staphylococcus aureus)
Go to UniProtKB:  W8UVN7
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
N
57Staphylococcus aureusMutation(s): 0 
Gene Names: rpmF
Find proteins for A0A077UWR7 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UWR7
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
O
49Staphylococcus aureusMutation(s): 0 
Gene Names: rpmG (rpmG_2)
Find proteins for A0A077UXT4 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UXT4
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
P
50Staphylococcus aureus subsp. aureus CN1Mutation(s): 0 
Gene Names: rpmH
Find proteins for T1YD75 (Staphylococcus aureus subsp. aureus CN1)
Go to UniProtKB:  T1YD75
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
Q
65Staphylococcus aureusMutation(s): 0 
Gene Names: rpmI (rpmI_2)
Find proteins for A0A077UL47 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UL47
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
R
37Staphylococcus aureusMutation(s): 0 
Gene Names: rpmJ (rpmJ_1)
Find proteins for A0A077UGV8 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UGV8
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
S
207Staphylococcus aureusMutation(s): 0 
Gene Names: rplD
Find proteins for A0A166DK89 (Staphylococcus aureus)
Go to UniProtKB:  A0A166DK89
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
V
145Staphylococcus aureusMutation(s): 0 
Gene Names: rplM (rplM_1, rplM_2, rplM_3, rplM_4)
Find proteins for W8TUE6 (Staphylococcus aureus)
Go to UniProtKB:  W8TUE6
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
W
122Staphylococcus aureusMutation(s): 0 
Gene Names: rplN (rplN_1, rplNA)
Find proteins for A0A077UUA0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UUA0
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
X
146Staphylococcus aureusMutation(s): 0 
Gene Names: rplO (rplO_1)
Find proteins for A0A077UGA7 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UGA7
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
Y
144Staphylococcus aureusMutation(s): 0 
Gene Names: rplP (rplP_1)
Find proteins for A0A077V4G0 (Staphylococcus aureus)
Go to UniProtKB:  A0A077V4G0
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
Z
122Staphylococcus aureusMutation(s): 0 
Gene Names: rplQ (rplQ_1, rplQ_2)
Find proteins for A0A077UG91 (Staphylococcus aureus)
Go to UniProtKB:  A0A077UG91
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
a
119Staphylococcus aureusMutation(s): 0 
Gene Names: rplR (rplR_1)
Find proteins for W8TRE0 (Staphylococcus aureus)
Go to UniProtKB:  W8TRE0
Entity ID: 26
MoleculeChainsLengthOrganism
23S rRNA12923Staphylococcus aureus
Entity ID: 27
MoleculeChainsLengthOrganism
5S rRNA2115Staphylococcus aureus
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G6V
Query on G6V

Download SDF File 
Download CCD File 
1
2,2-dichloro-N-({(5S)-3-[3-fluoro-4-(morpholin-4-yl)phenyl]-2-oxo-1,3-oxazolidin-5-yl}methyl)acetamide
oxazolidinone antibiotic LZD-5
C16 H18 Cl2 F N3 O4
YEXPTKNKQPHGOQ-NSHDSACASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Health and Medical Research Council (Australia)AustraliaProgram Grant 1092262

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release