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Bacterial 30S ribosomal subunit assembly complex state C (body domain)

Analyse Bacterial 30S ribosomal subunit assembly complex state C (body domain) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7AFI
Type: protein + RNA
Length: 2,453 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16SRRNA; 30S ribosomal protein S4; 30S ribosomal protein S5; 30S ribosomal protein S6…
UniProt: C3SR62, C3SR27, P02358, C3SR12, C3SR57, C3SQR7, C3SSQ7, C3SYP2, C3SQY7, C3SFP7, C3TRH7, A0A0J3VRH1
Ligands: MG
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 13 distinct chains · 35% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	16SRRNA	rna	1066	—	—
D	30S ribosomal protein S4	protein	205	44% helix, 8% strand	C3SR62
E	30S ribosomal protein S5	protein	156	30% helix, 34% strand	C3SR27
F	30S ribosomal protein S6	protein	106	35% helix, 34% strand	P02358
H	30S ribosomal protein S8	protein	129	29% helix, 30% strand	C3SR12
K	30S ribosomal protein S11	protein	116	31% helix, 25% strand	C3SR57
L	30S ribosomal protein S12	protein	123	10% helix, 26% strand	C3SQR7
O	30S ribosomal protein S15	protein	88	73% helix, 0% strand	C3SSQ7
P	30S ribosomal protein S16	protein	82	26% helix, 38% strand	C3SYP2
Q	30S ribosomal protein S17	protein	80	4% helix, 51% strand	C3SQY7
R	30S ribosomal protein S18	protein	65	48% helix, 6% strand	C3SFP7
T	30S ribosomal protein S20	protein	86	85% helix, 0% strand	C3TRH7
X	Ribosome maturation factor rimp	protein	151	25% helix, 31% strand	A0A0J3VRH1

Ligands and binding sites

MG · Magnesium ion · metal · 46 copies · chains A, D, T, L, X

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	577	0.83	0.89	57	MG
2	814	0.83	0.86	63	MG
3	991	0.81	0.83	92	empty
4	825	0.80	0.84	63	MG
5	549	0.80	0.87	49	MG

Interfaces

20 interfaces between chains.

A–D · 3206 Å² buried · 90 hydrogen bonds · protein-nucleic
A–L · 2564 Å² buried · 77 hydrogen bonds · protein-nucleic
A–T · 2198 Å² buried · 60 hydrogen bonds · protein-nucleic
A–P · 2165 Å² buried · 41 hydrogen bonds · protein-nucleic
A–K · 1953 Å² buried · 62 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 6 modified (nucleotide modification, nonstandard).

Compared structures

7AFI · Bacterial 30S ribosomal subunit assembly complex state C (body domain) · 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 C3SR62
Every structure of UniProt C3SR27
Every structure of UniProt P02358
Every structure of UniProt C3SR12
Every structure of UniProt C3SR57
Every structure of UniProt C3SQR7
Every structure of UniProt C3SSQ7
Every structure of UniProt C3SYP2
Every structure of UniProt C3SQY7
Every structure of UniProt C3SFP7
Every structure of UniProt C3TRH7
Every structure of UniProt A0A0J3VRH1
Elsewhere: RCSB PDB 7AFI · PDBe 7AFI · UniProt C3SR62 · UniProt C3SR27 · UniProt P02358 · UniProt C3SR12 · UniProt C3SR57 · UniProt C3SQR7 · UniProt C3SSQ7 · UniProt C3SYP2 · UniProt C3SQY7 · UniProt C3SFP7 · UniProt C3TRH7 · UniProt A0A0J3VRH1

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