MolNFT v1 · #165212 · protein + RNA

Mini-RNase III (mini-III) bound to 50S ribosome with precursor 23S rRNA

6TNN · 50S ribosomal protein L10: “Mini-RNase III (mini-III) bound to 50S ribosome with precursor 23S rRNA”. Electron microscopy, 2 ligands (MG, ZN), 20 pockets (best druggability 0.89). MolNFT v1 #165212 on GenesisL1: 3D structure…

PDB: 6TNN
Type: protein + RNA
Length: 6,406 residues
Chains: 31
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L10; Mini-ribonuclease 3; Pre-23S rRNA; 5S rRNA; 50S ribosomal…
EC: 3.1.26.-
UniProt: P42923, O31418, P42919, P42920, P42921, P12877, P46898, P70974, P12875, P19946, P14577, P20277, P46899, O31742, P55873, P26908, P42060, P42924, P0CI78, P05657, O34687, P56849, P05647, P55874, P20278, P37807, P12873, P19947
Ligands: MG, ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 31 distinct chains · 25% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
b	50S ribosomal protein L10	protein	123	36% helix, 2% strand	P42923
H	Mini-ribonuclease 3 (EC 3.1.26.-)	protein	132	67% helix, 0% strand	O31418
I	Mini-ribonuclease 3 (EC 3.1.26.-)	protein	134	67% helix, 0% strand	O31418
U	Pre-23S rRNA	rna	2930	—	—
V	5S rRNA	rna	116	—	—
W	50S ribosomal protein L2	protein	275	5% helix, 24% strand	P42919
X	50S ribosomal protein L3	protein	207	8% helix, 36% strand	P42920
Y	50S ribosomal protein L4	protein	205	28% helix, 11% strand	P42921
Z	50S ribosomal protein L5	protein	178	29% helix, 16% strand	P12877
a	50S ribosomal protein L6	protein	175	18% helix, 31% strand	P46898
c	50S ribosomal protein L13	protein	142	23% helix, 18% strand	P70974
d	50S ribosomal protein L14	protein	122	3% helix, 35% strand	P12875
e	50S ribosomal protein L15	protein	146	16% helix, 6% strand	P19946
f	50S ribosomal protein L16	protein	138	19% helix, 23% strand	P14577
g	50S ribosomal protein L17	protein	119	39% helix, 15% strand	P20277
h	50S ribosomal protein L18	protein	120	36% helix, 18% strand	P46899
i	50S ribosomal protein L19	protein	114	9% helix, 36% strand	O31742
j	50S ribosomal protein L20	protein	117	64% helix, 0% strand	P55873
k	50S ribosomal protein L21	protein	101	0% helix, 41% strand	P26908
l	50S ribosomal protein L22	protein	109	37% helix, 38% strand	P42060
m	50S ribosomal protein L23	protein	93	26% helix, 29% strand	P42924
n	50S ribosomal protein L24	protein	101	0% helix, 37% strand	P0CI78
o	50S ribosomal protein L27	protein	82	0% helix, 34% strand	P05657
p	50S ribosomal protein L32	protein	54	17% helix, 15% strand	O34687
q	50S ribosomal protein L33 1	protein	48	0% helix, 46% strand	P56849
r	50S ribosomal protein L34	protein	44	55% helix, 0% strand	P05647
s	50S ribosomal protein L35	protein	64	20% helix, 6% strand	P55874
t	50S ribosomal protein L36	protein	36	0% helix, 31% strand	P20278
u	50S ribosomal protein L28	protein	58	0% helix, 45% strand	P37807
v	50S ribosomal protein L29	protein	65	78% helix, 0% strand	P12873
w	50S ribosomal protein L30	protein	58	26% helix, 26% strand	P19947

Ligands and binding sites

MG · Magnesium ion · metal · 221 copies · chains I, U, e, W, Y, c, m, X, o, H, V, u
ZN · Zinc ion · metal · 3 copies · chains p, q, t

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	987	0.89	0.92	107	MG
2	891	0.88	0.91	63	MG
3	933	0.88	0.90	97	MG
4	1131	0.87	0.88	85	MG
5	726	0.86	0.90	73	MG

Interfaces

58 interfaces between chains.

U–W · 7206 Å² buried · 144 hydrogen bonds · protein-nucleic
U–X · 4954 Å² buried · 64 hydrogen bonds · protein-nucleic
U–e · 4361 Å² buried · 83 hydrogen bonds · protein-nucleic
U–Y · 4262 Å² buried · 68 hydrogen bonds · protein-nucleic
U–j · 3929 Å² buried · 60 hydrogen bonds · protein-nucleic

Compared structures

6TNN · Mini-RNase III (Mini-III) bound to 50S ribosome with precursor 23S rRNA · 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 P42923
Every structure of UniProt O31418
Every structure of UniProt P42919
Every structure of UniProt P42920
Every structure of UniProt P42921
Every structure of UniProt P12877
Every structure of UniProt P46898
Every structure of UniProt P70974
Every structure of UniProt P12875
Every structure of UniProt P19946
Every structure of UniProt P14577
Every structure of UniProt P20277
Every structure of UniProt P46899
Every structure of UniProt O31742
Every structure of UniProt P55873
Every structure of UniProt P26908
Every structure of UniProt P42060
Every structure of UniProt P42924
Every structure of UniProt P0CI78
Every structure of UniProt P05657
Every structure of UniProt O34687
Every structure of UniProt P56849
Every structure of UniProt P05647
Every structure of UniProt P55874
Every structure of UniProt P20278
Every structure of UniProt P37807
Every structure of UniProt P12873
Every structure of UniProt P19947
Elsewhere: RCSB PDB 6TNN · PDBe 6TNN · UniProt P42923 · UniProt O31418 · UniProt P42919 · UniProt P42920 · UniProt P42921 · UniProt P12877 · UniProt P46898 · UniProt P70974 · UniProt P12875 · UniProt P19946 · UniProt P14577 · UniProt P20277 · UniProt P46899 · UniProt O31742 · UniProt P55873 · UniProt P26908 · UniProt P42060 · UniProt P42924 · UniProt P0CI78 · UniProt P05657 · UniProt O34687 · UniProt P56849 · UniProt P05647 · UniProt P55874 · UniProt P20278 · UniProt P37807 · UniProt P12873 · UniProt P19947

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.