MolNFT v1 · #68036 · protein + RNA

Atomic model of the immature 50S subunit from bacillus subtilis (state II-a)

3J3W · Ribosome RNA 23S: “Atomic model of the immature 50S subunit from bacillus subtilis (state II-a)”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #68036 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 3J3W
Type: protein + RNA
Length: 5,130 residues
Chains: 20
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosome RNA 23S; 50S ribosomal protein L32; 50S ribosomal protein L2; 50S ribosomal…
UniProt: O34687, P42919, P20277, P46898, P70974, P12875, P19946, O31742, P55873, P42920, P26908, P42060, P42924, P0CI78, P12873, P05647, Q06797, Q06796, P42921
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 20 distinct chains · 21% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribosome RNA 23S	rna	2685	—	—
0	50S ribosomal protein L32	protein	55	15% helix, 11% strand	O34687
C	50S ribosomal protein L2	protein	277	1% helix, 24% strand	P42919
N	50S ribosomal protein L17	protein	120	52% helix, 13% strand	P20277
G	50S ribosomal protein L6	protein	163	22% helix, 39% strand	P46898
J	50S ribosomal protein L13	protein	143	21% helix, 13% strand	P70974
K	50S ribosomal protein L14	protein	122	8% helix, 39% strand	P12875
L	50S ribosomal protein L15	protein	146	8% helix, 8% strand	P19946
P	50S ribosomal protein L19	protein	112	6% helix, 3% strand	O31742
Q	50S ribosomal protein L20	protein	117	69% helix, 0% strand	P55873
D	50S ribosomal protein L3	protein	206	4% helix, 40% strand	P42920
R	50S ribosomal protein L21	protein	102	0% helix, 51% strand	P26908
S	50S ribosomal protein L22	protein	112	34% helix, 33% strand	P42060
T	50S ribosomal protein L23	protein	95	17% helix, 28% strand	P42924
U	50S ribosomal protein L24	protein	103	0% helix, 4% strand	P0CI78
X	50S ribosomal protein L29	protein	61	79% helix, 0% strand	P12873
2	50S ribosomal protein L34	protein	44	59% helix, 0% strand	P05647
5	50S ribosomal protein L1	protein	120	33% helix, 8% strand	Q06797
6	50S ribosomal protein L11	protein	141	27% helix, 16% strand	Q06796
E	50S ribosomal protein L4	protein	206	26% helix, 7% strand	P42921

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	850	0.87	0.91	77	empty
2	1149	0.85	0.87	84	empty
3	1168	0.85	0.87	99	empty
4	648	0.85	0.90	46	empty
5	801	0.84	0.88	63	empty

Interfaces

34 interfaces between chains.

A–C · 7056 Å² buried · 237 hydrogen bonds · protein-nucleic
A–D · 5299 Å² buried · 143 hydrogen bonds · protein-nucleic
A–L · 4892 Å² buried · 154 hydrogen bonds · protein-nucleic
A–E · 4679 Å² buried · 126 hydrogen bonds · protein-nucleic
A–Q · 4200 Å² buried · 89 hydrogen bonds · protein-nucleic

Compared structures

3J3W · Atomic model of the immature 50S subunit from Bacillus subtilis (state II-a) · the same entry in another collection · chain D against D, 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 O34687
Every structure of UniProt P42919
Every structure of UniProt P20277
Every structure of UniProt P46898
Every structure of UniProt P70974
Every structure of UniProt P12875
Every structure of UniProt P19946
Every structure of UniProt O31742
Every structure of UniProt P55873
Every structure of UniProt P42920
Every structure of UniProt P26908
Every structure of UniProt P42060
Every structure of UniProt P42924
Every structure of UniProt P0CI78
Every structure of UniProt P12873
Every structure of UniProt P05647
Every structure of UniProt Q06797
Every structure of UniProt Q06796
Every structure of UniProt P42921
Elsewhere: RCSB PDB 3J3W · PDBe 3J3W · UniProt O34687 · UniProt P42919 · UniProt P20277 · UniProt P46898 · UniProt P70974 · UniProt P12875 · UniProt P19946 · UniProt O31742 · UniProt P55873 · UniProt P42920 · UniProt P26908 · UniProt P42060 · UniProt P42924 · UniProt P0CI78 · UniProt P12873 · UniProt P05647 · UniProt Q06797 · UniProt Q06796 · UniProt P42921

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