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Bacterial 30S ribosomal subunit assembly complex state a (multibody refinement for body domain of 30S ribosome)

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

PDB: 7NAS
Type: protein + RNA
Length: 2,428 residues
Chains: 14
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16S rRNA; 30S ribosomal protein S4; 30S ribosomal protein S5; 30S ribosomal protein S6…
UniProt: P0A7V8, P0A7W1, P02358, P0A7W7, P0A7R9, P0A7S3, P0ADZ4, P0A7T3, P0AG63, P0A7T7, P0A7U7, P68679, P0A8A8
Ligands: MG
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 14 distinct chains · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	16S rRNA	rna	974	—	—
D	30S ribosomal protein S4	protein	205	43% helix, 10% strand	P0A7V8
E	30S ribosomal protein S5	protein	156	26% helix, 35% strand	P0A7W1
F	30S ribosomal protein S6	protein	106	31% helix, 29% strand	P02358
H	30S ribosomal protein S8	protein	129	29% helix, 31% strand	P0A7W7
K	30S ribosomal protein S11	protein	117	25% helix, 23% strand	P0A7R9
L	30S ribosomal protein S12	protein	123	11% helix, 27% strand	P0A7S3
O	30S ribosomal protein S15	protein	88	74% helix, 0% strand	P0ADZ4
P	30S ribosomal protein S16	protein	82	27% helix, 34% strand	P0A7T3
Q	30S ribosomal protein S17	protein	80	4% helix, 50% strand	P0AG63
R	30S ribosomal protein S18	protein	65	49% helix, 0% strand	P0A7T7
T	30S ribosomal protein S20	protein	86	86% helix, 0% strand	P0A7U7
U	30S ribosomal protein S21	protein	66	70% helix, 3% strand	P68679
X	Ribosome maturation factor rimp	protein	151	26% helix, 35% strand	P0A8A8

Ligands and binding sites

MG · Magnesium ion · metal · 43 copies · chains A, K, T, P

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	941	0.84	0.87	79	MG
2	516	0.83	0.90	51	empty
3	808	0.82	0.86	70	MG
4	855	0.82	0.86	64	MG
5	841	0.81	0.84	85	MG

Interfaces

23 interfaces between chains.

A–D · 3113 Å² buried · 108 hydrogen bonds · protein-nucleic
A–L · 2617 Å² buried · 71 hydrogen bonds · protein-nucleic
A–P · 2063 Å² buried · 41 hydrogen bonds · protein-nucleic
A–T · 1952 Å² buried · 60 hydrogen bonds · protein-nucleic
A–K · 1906 Å² buried · 60 hydrogen bonds · protein-nucleic

Modifications

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

Compared structures

7NAS · Bacterial 30S ribosomal subunit assembly complex state A (multibody refinement for body… · the same entry in another collection · chain X against X, 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 P0A7V8
Every structure of UniProt P0A7W1
Every structure of UniProt P02358
Every structure of UniProt P0A7W7
Every structure of UniProt P0A7R9
Every structure of UniProt P0A7S3
Every structure of UniProt P0ADZ4
Every structure of UniProt P0A7T3
Every structure of UniProt P0AG63
Every structure of UniProt P0A7T7
Every structure of UniProt P0A7U7
Every structure of UniProt P68679
Every structure of UniProt P0A8A8
Elsewhere: RCSB PDB 7NAS · PDBe 7NAS · UniProt P0A7V8 · UniProt P0A7W1 · UniProt P02358 · UniProt P0A7W7 · UniProt P0A7R9 · UniProt P0A7S3 · UniProt P0ADZ4 · UniProt P0A7T3 · UniProt P0AG63 · UniProt P0A7T7 · UniProt P0A7U7 · UniProt P68679 · UniProt P0A8A8

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