MolNFT v1 · #173958 · protein + RNA

Staphylococcus aureus 30S ribosomal subunit in presence of spermidine (head only)

7BGE · 16S ribosomal RNA: “Staphylococcus aureus 30S ribosomal subunit in presence of spermidine (head only)”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #173958 on GenesisL1: 3D structure, binding sites and…

PDB: 7BGE
Type: protein + RNA
Length: 1,344 residues
Chains: 9
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16S ribosomal RNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal…
UniProt: Q2FZ25, Q2FW12, P48940, Q2FW39, Q931G5, Q2FW30, Q2FW19, Q2FW10
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 9 distinct chains · 30% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	16S ribosomal RNA	rna	465	—	—
b	30S ribosomal protein S2	protein	107	30% helix, 6% strand	Q2FZ25
c	30S ribosomal protein S3	protein	202	31% helix, 27% strand	Q2FW12
g	30S ribosomal protein S7	protein	145	54% helix, 3% strand	P48940
i	30S ribosomal protein S9	protein	125	24% helix, 16% strand	Q2FW39
j	30S ribosomal protein S10	protein	97	24% helix, 33% strand	Q931G5
m	30S ribosomal protein S13	protein	72	22% helix, 0% strand	Q2FW30
n	30S ribosomal protein S14 type Z	protein	59	29% helix, 5% strand	Q2FW19
s	30S ribosomal protein S19	protein	72	7% helix, 21% strand	Q2FW10

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	1113	0.86	0.88	93	empty
2	1088	0.84	0.86	81	empty
3	791	0.82	0.86	52	empty
4	802	0.81	0.85	47	empty
5	603	0.78	0.85	31	empty

Interfaces

16 interfaces between chains.

a–i · 3056 Å² buried · 58 hydrogen bonds · protein-nucleic
a–m · 2145 Å² buried · 45 hydrogen bonds · protein-nucleic
a–n · 2136 Å² buried · 38 hydrogen bonds · protein-nucleic
a–j · 2003 Å² buried · 36 hydrogen bonds · protein-nucleic
a–g · 1626 Å² buried · 37 hydrogen bonds · protein-nucleic

Compared structures

7BGE · Staphylococcus aureus 30S ribosomal subunit in presence of spermidine (head only) · the same entry in another collection · chain s against s, TM-score 1.00
Q2FW12 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S3 (Q2FW12) · a predicted model of the same protein · chain c against A, TM-score 0.98
P48940 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S7 (P48940) · a predicted model of the same protein · chain g against A, TM-score 0.97
Q931G5 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S10 (Q931G5) · a predicted model of the same protein · chain j against A, TM-score 0.95

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 P48940
Every structure of UniProt Q2FW39
Every structure of UniProt Q931G5
Every structure of UniProt Q2FW30
Every structure of UniProt Q2FW19
Every structure of UniProt Q2FW10
Elsewhere: RCSB PDB 7BGE · PDBe 7BGE · UniProt Q2FZ25 · UniProt Q2FW12 · UniProt P48940 · UniProt Q2FW39 · UniProt Q931G5 · UniProt Q2FW30 · UniProt Q2FW19 · UniProt Q2FW10

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