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Structure of the 50S subunit of the ribosome from methicillin resistant staphylococcus aureus in complex with an isomer of the tedizolid

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: 6WRU
Type: protein + RNA
Length: 5,609 residues
Chains: 28
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, W8U3X2, W8TUE6, A0A077UUA0, A0A077UGA7, A0A077V4G0, A0A077UG91, W8TRE0, A0A077ULC5
Ligands: U7Y
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 28 distinct chains · 20% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	50S ribosomal protein L19	protein	113	5% helix, 43% strand	A0A077UVB6
B	50S ribosomal protein L2	protein	275	4% helix, 25% strand	A0A077W1J0
C	50S ribosomal protein L20	protein	116	77% helix, 0% strand	A0A077VMP6
D	50S ribosomal protein L21	protein	100	0% helix, 55% strand	A0A0E0VQU6
E	50S ribosomal protein L22	protein	111	36% helix, 35% strand	A0A077UKF9
F	50S ribosomal protein L23	protein	87	13% helix, 37% strand	W8TUB4
G	50S ribosomal protein L24	protein	89	3% helix, 44% strand	W8TRD5
H	UL25	protein	93	20% helix, 35% strand	A0A2X2JWH5
J	50S ribosomal protein L28	protein	59	7% helix, 47% strand	A0A077URJ8
K	50S ribosomal protein L29	protein	58	76% helix, 0% strand	A0A2S6DIY7
L	50S ribosomal protein L3	protein	215	7% helix, 33% strand	W8U3W0
M	50S ribosomal protein L30	protein	56	32% helix, 23% strand	W8UVN7
N	50S ribosomal protein L32	protein	50	10% helix, 14% strand	A0A077UWR7
O	50S ribosomal protein L33	protein	47	0% helix, 49% strand	A0A077UXT4
P	50S ribosomal protein L34	protein	44	57% helix, 0% strand	T1YD75
Q	50S ribosomal protein L35	protein	64	9% helix, 6% strand	A0A077UL47
R	50S ribosomal protein L36	protein	37	8% helix, 38% strand	A0A077UGV8
S	50S ribosomal protein L4	protein	192	28% helix, 7% strand	A0A166DK89
U	50S ribosomal protein L6	protein	174	18% helix, 33% strand	W8U3X2
V	50S ribosomal protein L13	protein	143	27% helix, 19% strand	W8TUE6
W	50S ribosomal protein L14	protein	121	3% helix, 37% strand	A0A077UUA0
X	50S ribosomal protein L15	protein	144	16% helix, 14% strand	A0A077UGA7
Y	50S ribosomal protein L16	protein	136	19% helix, 28% strand	A0A077V4G0
Z	50S ribosomal protein L17	protein	114	47% helix, 18% strand	A0A077UG91
a	50S ribosomal protein L18	protein	116	32% helix, 16% strand	W8TRE0
1	23S rRNA	rna	2665	—	—
2	5S rRNA	rna	112	—	—
I	50S ribosomal protein L27	protein	78	0% helix, 41% strand	A0A077ULC5

Ligands and binding sites

U7Y · Tedizolid isomer · 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	890	0.87	0.90	68	empty
2	1010	0.87	0.89	86	empty
3	900	0.87	0.90	94	empty
4	727	0.85	0.90	80	empty
5	857	0.85	0.88	74	empty

Interfaces

51 interfaces between chains.

B–1 · 7061 Å² buried · 143 hydrogen bonds · protein-nucleic
L–1 · 5149 Å² buried · 91 hydrogen bonds · protein-nucleic
X–1 · 4569 Å² buried · 83 hydrogen bonds · protein-nucleic
S–1 · 4352 Å² buried · 79 hydrogen bonds · protein-nucleic
C–1 · 4018 Å² buried · 76 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6WRU · 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 W8U3X2
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 6WRU · PDBe 6WRU · 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 W8U3X2 · UniProt W8TUE6 · UniProt A0A077UUA0 · UniProt A0A077UGA7 · UniProt A0A077V4G0 · UniProt A0A077UG91 · UniProt W8TRE0 · UniProt A0A077ULC5

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