MolNFT v1 · #158319 · protein + RNA

Role of era in assembly and homeostasis of the ribosomal small subunit

6NQB · 30S ribosomal protein S3: “Role of era in assembly and homeostasis of the ribosomal small subunit”. Electron microscopy, 1 ligand (MG), 20 pockets (best druggability 0.83). MolNFT v1 #158319 on GenesisL1: 3D structure, binding sites…

PDB: 6NQB
Type: protein + RNA
Length: 3,093 residues
Chains: 16
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 30S ribosomal protein S3; 30S ribosomal protein S10; 30S ribosomal protein S14; 30S…
UniProt: A0A376HTV6, D7X302, A0A090BZT4, F4SQ43, L3PZ69, A1AGJ2, A0A074QGH8, D8A1L7, V6FZ95, Q8X9M2, S0UHH0, A0A0G3QJD8, D7ZI16, T6N332, U9ZNW8
Ligands: MG
Pockets: 20 · best druggability 0.83

Structure

electron microscopy · 16 distinct chains · 27% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	30S ribosomal protein S3	protein	206	25% helix, 17% strand	A0A376HTV6
J	30S ribosomal protein S10	protein	98	7% helix, 23% strand	D7X302
N	30S ribosomal protein S14	protein	96	33% helix, 2% strand	A0A090BZT4
S	30S ribosomal protein S19	protein	74	14% helix, 8% strand	F4SQ43
A	16S ribosomal RNA	rna	1341	—	—
D	30S ribosomal protein S4	protein	205	37% helix, 7% strand	L3PZ69
E	30S ribosomal protein S5	protein	149	28% helix, 25% strand	A1AGJ2
F	30S ribosomal protein S6	protein	77	23% helix, 12% strand	A0A074QGH8
H	30S ribosomal protein S8	protein	129	19% helix, 20% strand	D8A1L7
L	30S ribosomal protein S12	protein	123	3% helix, 14% strand	V6FZ95
O	30S ribosomal protein S15	protein	86	63% helix, 0% strand	Q8X9M2
P	30S ribosomal protein BS16	protein	79	24% helix, 19% strand	S0UHH0
Q	30S ribosomal protein S17	protein	79	0% helix, 47% strand	A0A0G3QJD8
R	30S ribosomal protein S18	protein	49	43% helix, 4% strand	D7ZI16
T	30S ribosomal protein S20	protein	85	73% helix, 0% strand	T6N332
B	30S ribosomal protein S2	protein	217	27% helix, 8% strand	U9ZNW8

Ligands and binding sites

MG · Magnesium ion · metal · chains A

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	1135	0.83	0.85	87	empty
2	940	0.83	0.86	70	empty
3	936	0.82	0.84	73	empty
4	849	0.82	0.85	73	empty
5	1097	0.82	0.84	80	empty

Interfaces

30 interfaces between chains.

A–D · 2994 Å² buried · 69 hydrogen bonds · protein-nucleic
A–L · 2880 Å² buried · 64 hydrogen bonds · protein-nucleic
A–P · 2304 Å² buried · 38 hydrogen bonds · protein-nucleic
N–A · 2200 Å² buried · 54 hydrogen bonds · protein-nucleic
A–T · 1855 Å² buried · 37 hydrogen bonds · protein-nucleic

Compared structures

6NQB · Role of Era in Assembly and Homeostasis of the Ribosomal Small Subunit · the same entry in another collection · chain B against B, 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 A0A376HTV6
Every structure of UniProt D7X302
Every structure of UniProt A0A090BZT4
Every structure of UniProt F4SQ43
Every structure of UniProt L3PZ69
Every structure of UniProt A1AGJ2
Every structure of UniProt A0A074QGH8
Every structure of UniProt D8A1L7
Every structure of UniProt V6FZ95
Every structure of UniProt Q8X9M2
Every structure of UniProt S0UHH0
Every structure of UniProt A0A0G3QJD8
Every structure of UniProt D7ZI16
Every structure of UniProt T6N332
Every structure of UniProt U9ZNW8
Elsewhere: RCSB PDB 6NQB · PDBe 6NQB · UniProt A0A376HTV6 · UniProt D7X302 · UniProt A0A090BZT4 · UniProt F4SQ43 · UniProt L3PZ69 · UniProt A1AGJ2 · UniProt A0A074QGH8 · UniProt D8A1L7 · UniProt V6FZ95 · UniProt Q8X9M2 · UniProt S0UHH0 · UniProt A0A0G3QJD8 · UniProt D7ZI16 · UniProt T6N332 · UniProt U9ZNW8

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