Research workbench

Structure of the 50S ribosomal subunit from methicillin resistant staphylococcus aureus in complex with the oxazolidinone antibiotic lzd-5

Analyse Structure of the 50S ribosomal subunit 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: 6DDD
Type: protein + RNA
Length: 5,318 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, B3VKN3, A0A077VMP6, D7URR3, A0A077UKF9, W8TUB4, W8TRD5, A0A133Q8Z9, A0A077ULC5, A0A077URJ8, A0A077W1J5, W8U3W0, W8UVN7, A0A077UWR7, A0A077UXT4, T1YD75, A0A077UL47, A0A077UGV8, A0A166DK89, W8TUE6, A0A077UUA0, A0A077UGA7, A0A077V4G0, A0A077UG91, W8TRE0
Ligands: G6V
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 27 distinct chains · 20% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	50S ribosomal protein L19	protein	113	4% helix, 37% strand	A0A077UVB6
B	50S ribosomal protein L2	protein	274	5% helix, 20% strand	B3VKN3
C	50S ribosomal protein L20	protein	116	71% helix, 0% strand	A0A077VMP6
D	50S ribosomal protein L21	protein	100	0% helix, 55% strand	D7URR3
E	50S ribosomal protein L22	protein	111	30% helix, 33% strand	A0A077UKF9
F	50S ribosomal protein L23	protein	87	13% helix, 34% strand	W8TUB4
G	50S ribosomal protein L24	protein	95	3% helix, 40% strand	W8TRD5
H	50S ribosomal protein L25	protein	93	18% helix, 34% strand	A0A133Q8Z9
I	50S ribosomal protein L27	protein	77	0% helix, 38% strand	A0A077ULC5
J	50S ribosomal protein L28	protein	59	0% helix, 44% strand	A0A077URJ8
K	50S ribosomal protein L29	protein	57	75% helix, 0% strand	A0A077W1J5
L	50S ribosomal protein L3	protein	215	8% helix, 33% strand	W8U3W0
M	50S ribosomal protein L30	protein	56	30% helix, 14% strand	W8UVN7
N	50S ribosomal protein L32	protein	50	16% helix, 12% strand	A0A077UWR7
O	50S ribosomal protein L33	protein	46	0% helix, 52% strand	A0A077UXT4
P	50S ribosomal protein L34	protein	44	59% helix, 0% strand	T1YD75
Q	50S ribosomal protein L35	protein	64	19% helix, 11% strand	A0A077UL47
R	50S ribosomal protein L36	protein	37	8% helix, 38% strand	A0A077UGV8
S	50S ribosomal protein L4	protein	171	36% helix, 9% strand	A0A166DK89
V	50S ribosomal protein L13	protein	143	30% helix, 19% strand	W8TUE6
W	50S ribosomal protein L14	protein	112	9% helix, 38% strand	A0A077UUA0
X	50S ribosomal protein L15	protein	125	14% helix, 6% strand	A0A077UGA7
Y	50S ribosomal protein L16	protein	136	18% helix, 27% strand	A0A077V4G0
Z	50S ribosomal protein L17	protein	114	46% helix, 18% strand	A0A077UG91
a	50S ribosomal protein L18	protein	73	22% helix, 22% strand	W8TRE0
1	23S rRNA	rna	2646	—	—
2	5S rRNA	rna	104	—	—

Ligands and binding sites

G6V · 2,2-dichloro-N-({(5S)-3-[3-fluoro-4-(morpholin-4-yl) phenyl]-2-oxo-1,3-oxazolidin-5-yl}methyl)acetamide · 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	901	0.88	0.91	94	empty
2	1160	0.87	0.89	99	empty
3	959	0.87	0.90	78	empty
4	1072	0.86	0.88	84	empty
5	1032	0.85	0.87	83	empty

Interfaces

51 interfaces between chains.

B–1 · 6918 Å² buried · 153 hydrogen bonds · protein-nucleic
L–1 · 5028 Å² buried · 83 hydrogen bonds · protein-nucleic
X–1 · 4542 Å² buried · 99 hydrogen bonds · protein-nucleic
S–1 · 4367 Å² buried · 84 hydrogen bonds · protein-nucleic
C–1 · 3972 Å² buried · 89 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

6DDD · Structure of the 50S ribosomal subunit from Methicillin Resistant Staphylococcus aureus… · the same entry in another collection · chain A against A, 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 B3VKN3
Every structure of UniProt A0A077VMP6
Every structure of UniProt D7URR3
Every structure of UniProt A0A077UKF9
Every structure of UniProt W8TUB4
Every structure of UniProt W8TRD5
Every structure of UniProt A0A133Q8Z9
Every structure of UniProt A0A077ULC5
Every structure of UniProt A0A077URJ8
Every structure of UniProt A0A077W1J5
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
Elsewhere: RCSB PDB 6DDD · PDBe 6DDD · UniProt A0A077UVB6 · UniProt B3VKN3 · UniProt A0A077VMP6 · UniProt D7URR3 · UniProt A0A077UKF9 · UniProt W8TUB4 · UniProt W8TRD5 · UniProt A0A133Q8Z9 · UniProt A0A077ULC5 · UniProt A0A077URJ8 · UniProt A0A077W1J5 · 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

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