Research workbench

Staphylococcus aureus 30S ribosomal subunit in presence of spermidine

Analyse Staphylococcus aureus 30S ribosomal subunit in presence of spermidine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KWG
Type: protein + RNA
Length: 3,835 residues
Chains: 21
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MRNA; 16S ribosomal RNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S…
UniProt: Q2FZ25, Q2FW12, Q2FXK6, Q2FW23, Q2G113, P48940, Q2FW20, Q2FW39, A0A380EDM5, Q2FW31, P0A0H0, Q2FW30, Q2FW19, Q2G2Q1, Q2FZ45, Q2FW15, Q2G111, Q2FW10, Q2FXY6
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 21 distinct chains · 29% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MRNA	rna	32	—	—
a	16S ribosomal RNA	rna	1552	—	—
b	30S ribosomal protein S2	protein	224	37% helix, 9% strand	Q2FZ25
c	30S ribosomal protein S3	protein	202	35% helix, 30% strand	Q2FW12
d	30S ribosomal protein S4	protein	196	36% helix, 7% strand	Q2FXK6
e	30S ribosomal protein S5	protein	165	21% helix, 25% strand	Q2FW23
f	30S ribosomal protein S6	protein	96	22% helix, 33% strand	Q2G113
g	30S ribosomal protein S7	protein	145	50% helix, 4% strand	P48940
h	30S ribosomal protein S8	protein	131	23% helix, 26% strand	Q2FW20
i	30S ribosomal protein S9	protein	125	24% helix, 12% strand	Q2FW39
j	30S ribosomal protein S10	protein	97	22% helix, 35% strand	A0A380EDM5
k	30S ribosomal protein S11	protein	118	25% helix, 26% strand	Q2FW31
l	30S ribosomal protein S12	protein	135	3% helix, 21% strand	P0A0H0
m	30S ribosomal protein S13	protein	72	22% helix, 0% strand	Q2FW30
n	30S ribosomal protein S14 type Z	protein	59	25% helix, 3% strand	Q2FW19
o	30S ribosomal protein S15	protein	88	67% helix, 0% strand	Q2G2Q1
p	30S ribosomal protein S16	protein	90	29% helix, 26% strand	Q2FZ45
q	30S ribosomal protein S17	protein	86	0% helix, 50% strand	Q2FW15
r	30S ribosomal protein S18	protein	70	34% helix, 3% strand	Q2G111
s	30S ribosomal protein S19	protein	72	6% helix, 18% strand	Q2FW10
t	30S ribosomal protein S20	protein	80	59% helix, 0% strand	Q2FXY6

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	831	0.86	0.90	68	empty
2	1045	0.86	0.88	89	empty
3	1030	0.86	0.88	88	empty
4	1064	0.86	0.88	88	empty
5	941	0.85	0.87	72	empty

Interfaces

46 interfaces between chains.

a–l · 3548 Å² buried · 75 hydrogen bonds · protein-nucleic
a–d · 3232 Å² buried · 73 hydrogen bonds · protein-nucleic
a–i · 3104 Å² buried · 57 hydrogen bonds · protein-nucleic
a–p · 2656 Å² buried · 49 hydrogen bonds · protein-nucleic
a–t · 2560 Å² buried · 44 hydrogen bonds · protein-nucleic

Compared structures

7KWG · Staphylococcus aureus 30S ribosomal subunit in presence of spermidine · the same entry in another collection · chain i against i, 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 Q2FZ25
Every structure of UniProt Q2FW12
Every structure of UniProt Q2FXK6
Every structure of UniProt Q2FW23
Every structure of UniProt Q2G113
Every structure of UniProt P48940
Every structure of UniProt Q2FW20
Every structure of UniProt Q2FW39
Every structure of UniProt A0A380EDM5
Every structure of UniProt Q2FW31
Every structure of UniProt P0A0H0
Every structure of UniProt Q2FW30
Every structure of UniProt Q2FW19
Every structure of UniProt Q2G2Q1
Every structure of UniProt Q2FZ45
Every structure of UniProt Q2FW15
Every structure of UniProt Q2G111
Every structure of UniProt Q2FW10
Every structure of UniProt Q2FXY6
Elsewhere: RCSB PDB 7KWG · PDBe 7KWG · UniProt Q2FZ25 · UniProt Q2FW12 · UniProt Q2FXK6 · UniProt Q2FW23 · UniProt Q2G113 · UniProt P48940 · UniProt Q2FW20 · UniProt Q2FW39 · UniProt A0A380EDM5 · UniProt Q2FW31 · UniProt P0A0H0 · UniProt Q2FW30 · UniProt Q2FW19 · UniProt Q2G2Q1 · UniProt Q2FZ45 · UniProt Q2FW15 · UniProt Q2G111 · UniProt Q2FW10 · UniProt Q2FXY6

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