Research workbench

Structure of the 50S subunit of the ribosome from methicillin resistant staphylococcus aureus in complex with the antibiotic, radezolid

Analyse Structure of the 50S subunit of the ribosome from methicillin resistant… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WQQ
Type: protein + RNA
Length: 5,480 residues
Chains: 27
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L19; 50S ribosomal protein L2; 50S ribosomal protein L20; 50S…
UniProt: A0A077UVB6, A0A077W1J0, A0A077VMP6, A0A0E0VQU6, A0A077UKF9, W8TUB4, W8TRD5, A0A2X2JWH5, A0A077URJ8, A0A2S6DIY7, W8U3W0, W8UVN7, A0A077UWR7, A0A077UXT4, T1YD75, A0A077UL47, A0A077UGV8, A0A166DK89, W8TUE6, A0A077UUA0, A0A077UGA7, A0A077V4G0, A0A077UG91, W8TRE0, A0A077ULC5
Ligands: RD8
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 27 distinct chains · 21% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	50S ribosomal protein L19	protein	113	12% helix, 38% strand	A0A077UVB6
B	50S ribosomal protein L2	protein	274	6% helix, 28% strand	A0A077W1J0
C	50S ribosomal protein L20	protein	116	77% helix, 0% strand	A0A077VMP6
D	50S ribosomal protein L21	protein	100	0% helix, 53% strand	A0A0E0VQU6
E	50S ribosomal protein L22	protein	111	39% helix, 35% strand	A0A077UKF9
F	50S ribosomal protein L23	protein	87	14% helix, 39% strand	W8TUB4
G	50S ribosomal protein L24	protein	100	3% helix, 37% strand	W8TRD5
H	50S ribosomal protein L25	protein	93	25% helix, 45% strand	A0A2X2JWH5
J	50S ribosomal protein L28	protein	59	7% helix, 34% strand	A0A077URJ8
K	50S ribosomal protein L29	protein	60	68% helix, 0% strand	A0A2S6DIY7
L	50S ribosomal protein L3	protein	215	6% helix, 33% strand	W8U3W0
M	50S ribosomal protein L30	protein	56	27% helix, 21% strand	W8UVN7
N	50S ribosomal protein L32	protein	50	14% helix, 12% strand	A0A077UWR7
O	50S ribosomal protein L33	protein	47	0% helix, 53% strand	A0A077UXT4
P	50S ribosomal protein L34	protein	44	50% helix, 0% strand	T1YD75
Q	50S ribosomal protein L35	protein	64	23% helix, 13% strand	A0A077UL47
R	50S ribosomal protein L36	protein	37	0% helix, 32% strand	A0A077UGV8
S	50S ribosomal protein L4	protein	192	29% helix, 9% strand	A0A166DK89
V	50S ribosomal protein L13	protein	143	29% helix, 19% strand	W8TUE6
W	50S ribosomal protein L14	protein	121	5% helix, 36% strand	A0A077UUA0
X	50S ribosomal protein L15	protein	144	15% helix, 10% strand	A0A077UGA7
Y	50S ribosomal protein L16	protein	136	16% helix, 26% strand	A0A077V4G0
Z	50S ribosomal protein L17	protein	121	43% helix, 20% strand	A0A077UG91
a	50S ribosomal protein L18	protein	110	37% helix, 16% strand	W8TRE0
1	23S rRNA	rna	2698	—	—
2	5S rRNA	rna	111	—	—
I	50S ribosomal protein L27	protein	78	0% helix, 35% strand	A0A077ULC5

Ligands and binding sites

RD8 · Radezolid · ligand · chains 1

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	967	0.88	0.91	94	empty
2	911	0.88	0.91	94	empty
3	1159	0.87	0.89	78	empty
4	582	0.87	0.93	78	empty
5	848	0.85	0.88	72	empty

Interfaces

50 interfaces between chains.

B–1 · 6979 Å² buried · 136 hydrogen bonds · protein-nucleic
L–1 · 5048 Å² buried · 70 hydrogen bonds · protein-nucleic
X–1 · 4442 Å² buried · 77 hydrogen bonds · protein-nucleic
S–1 · 4268 Å² buried · 71 hydrogen bonds · protein-nucleic
C–1 · 3925 Å² buried · 80 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6WQQ · Structure of the 50S subunit of the ribosome from Methicillin Resistant Staphylococcus… · the same entry in another collection · chain B against B, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0A077UVB6
Every structure of UniProt A0A077W1J0
Every structure of UniProt A0A077VMP6
Every structure of UniProt A0A0E0VQU6
Every structure of UniProt A0A077UKF9
Every structure of UniProt W8TUB4
Every structure of UniProt W8TRD5
Every structure of UniProt A0A2X2JWH5
Every structure of UniProt A0A077URJ8
Every structure of UniProt A0A2S6DIY7
Every structure of UniProt W8U3W0
Every structure of UniProt W8UVN7
Every structure of UniProt A0A077UWR7
Every structure of UniProt A0A077UXT4
Every structure of UniProt T1YD75
Every structure of UniProt A0A077UL47
Every structure of UniProt A0A077UGV8
Every structure of UniProt A0A166DK89
Every structure of UniProt W8TUE6
Every structure of UniProt A0A077UUA0
Every structure of UniProt A0A077UGA7
Every structure of UniProt A0A077V4G0
Every structure of UniProt A0A077UG91
Every structure of UniProt W8TRE0
Every structure of UniProt A0A077ULC5
Elsewhere: RCSB PDB 6WQQ · PDBe 6WQQ · UniProt A0A077UVB6 · UniProt A0A077W1J0 · UniProt A0A077VMP6 · UniProt A0A0E0VQU6 · UniProt A0A077UKF9 · UniProt W8TUB4 · UniProt W8TRD5 · UniProt A0A2X2JWH5 · UniProt A0A077URJ8 · UniProt A0A2S6DIY7 · UniProt W8U3W0 · UniProt W8UVN7 · UniProt A0A077UWR7 · UniProt A0A077UXT4 · UniProt T1YD75 · UniProt A0A077UL47 · UniProt A0A077UGV8 · UniProt A0A166DK89 · UniProt W8TUE6 · UniProt A0A077UUA0 · UniProt A0A077UGA7 · UniProt A0A077V4G0 · UniProt A0A077UG91 · UniProt W8TRE0 · UniProt A0A077ULC5

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