MolNFT v1 · #168138 · protein + RNA

30S-activated-high-MG2+

6W6K · 16S rRNA: “30S-activated-high-MG2+”. Electron microscopy, 1 ligand (MG), 20 pockets (best druggability 0.86). MolNFT v1 #168138 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6W6K
Type: protein + RNA
Length: 3,407 residues
Chains: 18
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16S rRNA; 30S ribosomal protein S3; 30S ribosomal protein S4; 30S ribosomal protein S5…
UniProt: P0A7V3, P0A7V8, P0A7W1, P02358, P0A7W7, P0A7X3, P0A7R5, P0A7R9, P0A7S3, P0A7S9, P0AG59, A0A4S5B232, P0A7T3, P0AG63, P0A7T7, P0A7U3, P0A7U7
Ligands: MG
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 18 distinct chains · 28% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	16S rRNA	rna	1534	—	—
C	30S ribosomal protein S3	protein	206	30% helix, 17% strand	P0A7V3
D	30S ribosomal protein S4	protein	205	38% helix, 7% strand	P0A7V8
E	30S ribosomal protein S5	protein	149	26% helix, 27% strand	P0A7W1
F	30S ribosomal protein S6	protein	57	7% helix, 19% strand	P02358
H	30S ribosomal protein S8	protein	129	18% helix, 23% strand	P0A7W7
I	30S ribosomal protein S9	protein	127	22% helix, 13% strand	P0A7X3
J	30S ribosomal protein S10	protein	98	7% helix, 24% strand	P0A7R5
K	30S ribosomal protein S11	protein	117	18% helix, 21% strand	P0A7R9
L	30S ribosomal protein S12	protein	123	3% helix, 14% strand	P0A7S3
M	30S ribosomal protein S13	protein	114	46% helix, 0% strand	P0A7S9
N	30S ribosomal protein S14	protein	96	35% helix, 0% strand	P0AG59
O	30S ribosomal protein S15	protein	86	65% helix, 0% strand	A0A4S5B232
P	30S ribosomal protein S16	protein	79	24% helix, 14% strand	P0A7T3
Q	30S ribosomal protein S17	protein	79	0% helix, 51% strand	P0AG63
R	30S ribosomal protein S18	protein	49	41% helix, 4% strand	P0A7T7
S	30S ribosomal protein S19	protein	74	22% helix, 15% strand	P0A7U3
T	30S ribosomal protein S20	protein	85	81% helix, 0% strand	P0A7U7

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	1164	0.86	0.88	119	empty
2	1074	0.86	0.88	95	empty
3	1141	0.85	0.87	85	empty
4	794	0.84	0.88	61	empty
5	811	0.84	0.87	64	empty

Interfaces

32 interfaces between chains.

A–L · 3072 Å² buried · 72 hydrogen bonds · protein-nucleic
A–D · 2951 Å² buried · 49 hydrogen bonds · protein-nucleic
A–P · 2230 Å² buried · 31 hydrogen bonds · protein-nucleic
A–T · 2113 Å² buried · 22 hydrogen bonds · protein-nucleic
A–N · 1970 Å² buried · 29 hydrogen bonds · protein-nucleic

Compared structures

6W6K · 30S-Activated-high-Mg2+ · 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 P0A7V3
Every structure of UniProt P0A7V8
Every structure of UniProt P0A7W1
Every structure of UniProt P02358
Every structure of UniProt P0A7W7
Every structure of UniProt P0A7X3
Every structure of UniProt P0A7R5
Every structure of UniProt P0A7R9
Every structure of UniProt P0A7S3
Every structure of UniProt P0A7S9
Every structure of UniProt P0AG59
Every structure of UniProt A0A4S5B232
Every structure of UniProt P0A7T3
Every structure of UniProt P0AG63
Every structure of UniProt P0A7T7
Every structure of UniProt P0A7U3
Every structure of UniProt P0A7U7
Elsewhere: RCSB PDB 6W6K · PDBe 6W6K · UniProt P0A7V3 · UniProt P0A7V8 · UniProt P0A7W1 · UniProt P02358 · UniProt P0A7W7 · UniProt P0A7X3 · UniProt P0A7R5 · UniProt P0A7R9 · UniProt P0A7S3 · UniProt P0A7S9 · UniProt P0AG59 · UniProt A0A4S5B232 · UniProt P0A7T3 · UniProt P0AG63 · UniProt P0A7T7 · UniProt P0A7U3 · UniProt P0A7U7

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