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The crystal structure of the large ribosomal subunit of staphylococcus aureus

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: 4WCE
Type: protein + RNA
Length: 5,819 residues
Chains: 28
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S rRNA; 5S rRNA; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal…
UniProt: P60430, Q2YYP6, Q2FW07, Q2FW18, Q2FW21, Q2FW38, Q2FW16, P0A0F8, Q2FW13, Q2FW33, Q2FW22, Q2FZ42, Q2FXQ1, Q2FXS8, Q2FW11, Q2FW08, Q2FW17, Q2FJE0, Q2FXT0, Q2FZ60, Q2FW14, P0A0G2, Q2FZF1, Q2FUQ0, Q2FXQ0, Q2FW29
Ligands: SPD, MN, MG
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 28 distinct chains · 21% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	23S rRNA	rna	2708	—	—
Y	5S rRNA	rna	114	—	—
A	50S ribosomal protein L2	protein	269	3% helix, 13% strand	P60430
B	50S ribosomal protein L3	protein	215	9% helix, 34% strand	Q2YYP6
C	50S ribosomal protein L4	protein	199	28% helix, 11% strand	Q2FW07
D	50S ribosomal protein L5	protein	166	26% helix, 9% strand	Q2FW18
E	50S ribosomal protein L6	protein	156	20% helix, 6% strand	Q2FW21
G	50S ribosomal protein L13	protein	145	32% helix, 12% strand	Q2FW38
H	50S ribosomal protein L14	protein	122	8% helix, 34% strand	Q2FW16
I	50S ribosomal protein L15	protein	131	8% helix, 5% strand	P0A0F8
J	50S ribosomal protein L16	protein	141	18% helix, 23% strand	Q2FW13
K	50S ribosomal protein L17	protein	119	49% helix, 17% strand	Q2FW33
L	50S ribosomal protein L18	protein	110	27% helix, 5% strand	Q2FW22
M	50S ribosomal protein L19	protein	110	9% helix, 35% strand	Q2FZ42
N	50S ribosomal protein L20	protein	116	73% helix, 0% strand	Q2FXQ1
O	50S ribosomal protein L21	protein	102	0% helix, 37% strand	Q2FXS8
P	50S ribosomal protein L22	protein	112	38% helix, 38% strand	Q2FW11
Q	50S ribosomal protein L23	protein	89	21% helix, 25% strand	Q2FW08
R	50S ribosomal protein L24	protein	100	3% helix, 20% strand	Q2FW17
S	50S ribosomal protein L25	protein	167	9% helix, 32% strand	Q2FJE0
T	50S ribosomal protein L27	protein	75	0% helix, 39% strand	Q2FXT0
U	50S ribosomal protein L28	protein	46	0% helix, 30% strand	Q2FZ60
V	50S ribosomal protein L29	protein	65	66% helix, 0% strand	Q2FW14
W	50S ribosomal protein L30	protein	58	36% helix, 24% strand	P0A0G2
Z	50S ribosomal protein L32	protein	43	23% helix, 14% strand	Q2FZF1
2	50S ribosomal protein L34	protein	44	61% helix, 0% strand	Q2FUQ0
3	50S ribosomal protein L35	protein	60	22% helix, 10% strand	Q2FXQ0
4	50S ribosomal protein L36	protein	37	8% helix, 30% strand	Q2FW29

Ligands and binding sites

SPD · Spermidine · ligand · 4 copies · chains X, C, G
MN · Manganese (II) ion · metal · 231 copies · chains X, A, 2, G, J, M, Q, T, B, C, K, I, 4, Y, R
MG · Magnesium ion · metal · 91 copies · chains X, N, Y, C, B, G, O, I
MPD · (4S)-2-methyl-2,4-pentanediol · additive · 12 copies · chains X, C, U, N, I, Z
EOH · Ethanol · additive · 7 copies · chains X, R
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains X, G

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	982	0.88	0.91	99	MN, MG
2	1079	0.88	0.90	104	MPD, MN, MG
3	604	0.87	0.93	80	MPD, MG, MN
4	990	0.87	0.89	94	MN, MG, EPE
5	1010	0.86	0.88	89	MN

Interfaces

53 interfaces between chains.

X–A · 5918 Å² buried · 122 hydrogen bonds · protein-nucleic
X–B · 5046 Å² buried · 126 hydrogen bonds · protein-nucleic
X–C · 3965 Å² buried · 70 hydrogen bonds · protein-nucleic
X–N · 3956 Å² buried · 108 hydrogen bonds · protein-nucleic
X–I · 3658 Å² buried · 64 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

4WCE · The crystal structure of the large ribosomal subunit of Staphylococcus aureus · the same entry in another collection · chain H against H, 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 Q2YYP6
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 Q2FJE0
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 4WCE · PDBe 4WCE · UniProt P60430 · UniProt Q2YYP6 · 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 Q2FJE0 · UniProt Q2FXT0 · UniProt Q2FZ60 · UniProt Q2FW14 · UniProt P0A0G2 · UniProt Q2FZF1 · UniProt Q2FUQ0 · UniProt Q2FXQ0 · UniProt Q2FW29

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