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The crystal structure of the large ribosomal subunit of staphylococcus aureus in complex with lefamulin

Analyse The crystal structure of the large ribosomal subunit of staphylococcus aureus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5HL7
Type: protein + RNA
Length: 5,808 residues
Chains: 28
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L2; 23S ribosomal RNA; 5S ribosomal RNA; 50S ribosomal protein L3…
UniProt: P60430, Q2FW06, Q2FW07, Q2FW18, Q2FW21, Q2FW38, Q2FW16, P0A0F8, Q2FW13, Q2FW33, Q2FW22, Q2FZ42, Q2FXQ1, Q2FXS8, Q2FW11, Q2FW08, Q2FW17, Q2G0S0, Q2FXT0, Q2FZ60, Q2FW14, P0A0G2, Q2FZF1, Q2FUQ0, Q2FXQ0, Q2FW29
Ligands: SPD, 62B, MN, MG
Pockets: 20 · best druggability 0.90

Structure

x-ray diffraction · 28 distinct chains · 21% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	50S ribosomal protein L2	protein	269	6% helix, 16% strand	P60430
X	23S ribosomal RNA	rna	2705	—	—
Y	5S ribosomal RNA	rna	114	—	—
B	50S ribosomal protein L3	protein	215	9% helix, 35% strand	Q2FW06
C	50S ribosomal protein L4	protein	199	24% helix, 6% strand	Q2FW07
D	50S ribosomal protein L5	protein	165	26% helix, 11% strand	Q2FW18
E	50S ribosomal protein L6	protein	157	20% helix, 9% strand	Q2FW21
G	50S ribosomal protein L13	protein	145	28% helix, 14% strand	Q2FW38
H	50S ribosomal protein L14	protein	122	8% helix, 36% strand	Q2FW16
I	50S ribosomal protein L15	protein	131	11% helix, 7% strand	P0A0F8
J	50S ribosomal protein L16	protein	138	19% helix, 25% strand	Q2FW13
K	50S ribosomal protein L17	protein	119	48% helix, 18% strand	Q2FW33
L	50S ribosomal protein L18	protein	109	32% helix, 11% strand	Q2FW22
M	50S ribosomal protein L19	protein	110	11% helix, 38% strand	Q2FZ42
N	50S ribosomal protein L20	protein	116	72% helix, 0% strand	Q2FXQ1
O	50S ribosomal protein L21	protein	102	0% helix, 54% strand	Q2FXS8
P	50S ribosomal protein L22	protein	112	39% helix, 25% strand	Q2FW11
Q	50S ribosomal protein L23	protein	90	21% helix, 27% strand	Q2FW08
R	50S ribosomal protein L24	protein	102	0% helix, 21% strand	Q2FW17
S	50S ribosomal protein L25	protein	167	10% helix, 32% strand	Q2G0S0
T	50S ribosomal protein L27	protein	75	0% helix, 39% strand	Q2FXT0
U	50S ribosomal protein L28	protein	42	0% helix, 29% strand	Q2FZ60
V	50S ribosomal protein L29	protein	65	69% helix, 0% strand	Q2FW14
W	50S ribosomal protein L30	protein	57	37% helix, 23% strand	P0A0G2
Z	50S ribosomal protein L32	protein	43	23% helix, 14% strand	Q2FZF1
2	50S ribosomal protein L34	protein	43	60% helix, 0% strand	Q2FUQ0
3	50S ribosomal protein L35	protein	60	7% helix, 10% strand	Q2FXQ0
4	50S ribosomal protein L36	protein	36	8% helix, 31% strand	Q2FW29

Ligands and binding sites

SPD · Spermidine · ligand · 8 copies · chains X, Y
62B · Lefamulin · ligand · chains X
MN · Manganese (II) ion · metal · 274 copies · chains A, X, C, B, I, G, N, M, R, 2, J, O, Y, T, Z
MG · Magnesium ion · metal · 240 copies · chains A, X, G, K, 2, N, Q, C, Y, B, T, Z, S, I, 3, J, M, O, P
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 11 copies · chains X, M, G, J, S, Q, Z
EOH · Ethanol · additive · 3 copies · chains X, Y, S
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains X, N

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	896	0.90	0.93	105	MN, MG
2	801	0.87	0.91	79	MG, MN
3	841	0.87	0.91	71	MN, MG
4	877	0.85	0.88	97	MN, MG
5	441	0.85	0.93	56	empty

Interfaces

53 interfaces between chains.

A–X · 5924 Å² buried · 123 hydrogen bonds · protein-nucleic
X–B · 4959 Å² buried · 120 hydrogen bonds · protein-nucleic
X–C · 3936 Å² buried · 74 hydrogen bonds · protein-nucleic
X–N · 3835 Å² buried · 106 hydrogen bonds · protein-nucleic
X–I · 3360 Å² buried · 60 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5HL7 · The crystal structure of the large ribosomal subunit of Staphylococcus aureus in complex… · the same entry in another collection · chain D against D, 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 P60430
Every structure of UniProt Q2FW06
Every structure of UniProt Q2FW07
Every structure of UniProt Q2FW18
Every structure of UniProt Q2FW21
Every structure of UniProt Q2FW38
Every structure of UniProt Q2FW16
Every structure of UniProt P0A0F8
Every structure of UniProt Q2FW13
Every structure of UniProt Q2FW33
Every structure of UniProt Q2FW22
Every structure of UniProt Q2FZ42
Every structure of UniProt Q2FXQ1
Every structure of UniProt Q2FXS8
Every structure of UniProt Q2FW11
Every structure of UniProt Q2FW08
Every structure of UniProt Q2FW17
Every structure of UniProt Q2G0S0
Every structure of UniProt Q2FXT0
Every structure of UniProt Q2FZ60
Every structure of UniProt Q2FW14
Every structure of UniProt P0A0G2
Every structure of UniProt Q2FZF1
Every structure of UniProt Q2FUQ0
Every structure of UniProt Q2FXQ0
Every structure of UniProt Q2FW29
Elsewhere: RCSB PDB 5HL7 · PDBe 5HL7 · UniProt P60430 · UniProt Q2FW06 · UniProt Q2FW07 · UniProt Q2FW18 · UniProt Q2FW21 · UniProt Q2FW38 · UniProt Q2FW16 · UniProt P0A0F8 · UniProt Q2FW13 · UniProt Q2FW33 · UniProt Q2FW22 · UniProt Q2FZ42 · UniProt Q2FXQ1 · UniProt Q2FXS8 · UniProt Q2FW11 · UniProt Q2FW08 · UniProt Q2FW17 · UniProt Q2G0S0 · UniProt Q2FXT0 · UniProt Q2FZ60 · UniProt Q2FW14 · UniProt P0A0G2 · UniProt Q2FZF1 · UniProt Q2FUQ0 · UniProt Q2FXQ0 · UniProt Q2FW29

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