MolNFT v1 · #174210 · protein + RNA

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

7BOD · 16S rRNA (body domain of 30S subunit): “Bacterial 30S ribosomal subunit assembly complex state M (body domain)”. Electron microscopy, 1 ligand (MG), 20 pockets (best druggability 0.86). MolNFT v1 #174210 on GenesisL1: 3D structure…

PDB: 7BOD
Type: protein + RNA
Length: 2,367 residues
Chains: 13
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16S rRNA (body domain of 30S subunit); 30S ribosomal protein S4; 30S ribosomal protein…
UniProt: P0A7V8, P0A7W1, P02358, P0A7W7, P0A7R9, P0A7S3, P0ADZ4, P0A7T3, P0AG63, P0A7T7, P0A7U7, P68679
Ligands: MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 13 distinct chains · 36% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	16S rRNA (body domain of 30S subunit)	rna	1078	—	—
D	30S ribosomal protein S4	protein	205	41% helix, 10% strand	P0A7V8
E	30S ribosomal protein S5	protein	156	31% helix, 37% strand	P0A7W1
F	30S ribosomal protein S6	protein	106	34% helix, 34% strand	P02358
H	30S ribosomal protein S8	protein	129	27% helix, 29% strand	P0A7W7
K	30S ribosomal protein S11	protein	117	21% helix, 29% strand	P0A7R9
L	30S ribosomal protein S12	protein	123	7% helix, 28% strand	P0A7S3
O	30S ribosomal protein S15	protein	88	75% helix, 0% strand	P0ADZ4
P	30S ribosomal protein S16	protein	82	26% helix, 33% strand	P0A7T3
Q	30S ribosomal protein S17	protein	80	4% helix, 63% strand	P0AG63
R	30S ribosomal protein S18	protein	65	48% helix, 3% strand	P0A7T7
T	30S ribosomal protein S20	protein	86	78% helix, 0% strand	P0A7U7
U	30S ribosomal protein S21	protein	52	67% helix, 2% strand	P68679

Ligands and binding sites

MG · Magnesium ion · metal · 101 copies · chains A, K, Q, E, P, D

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	948	0.86	0.88	89	MG
2	975	0.84	0.86	88	MG
3	686	0.83	0.88	64	MG
4	839	0.83	0.86	74	MG
5	1164	0.82	0.84	110	MG

Interfaces

22 interfaces between chains.

A–D · 3192 Å² buried · 86 hydrogen bonds · protein-nucleic
A–L · 2969 Å² buried · 74 hydrogen bonds · protein-nucleic
A–T · 2393 Å² buried · 53 hydrogen bonds · protein-nucleic
A–P · 2153 Å² buried · 44 hydrogen bonds · protein-nucleic
A–K · 2031 Å² buried · 46 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 9 modified (nucleotide modification, nonstandard).

Compared structures

7BOD · Bacterial 30S ribosomal subunit assembly complex state M (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 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
Elsewhere: RCSB PDB 7BOD · PDBe 7BOD · UniProt P0A7V8 · UniProt P0A7W1 · UniProt P02358 · UniProt P0A7W7 · UniProt P0A7R9 · UniProt P0A7S3 · UniProt P0ADZ4 · UniProt P0A7T3 · UniProt P0AG63 · UniProt P0A7T7 · UniProt P0A7U7 · UniProt P68679

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