Research workbench

Cryo-EM image reconstruction of the 70S Ribosome Enterococcus faecalis Class02

Analyse Cryo-EM image reconstruction of the 70S Ribosome Enterococcus faecalis Class02 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6O8X
Type: protein + RNA
Length: 9,746 residues
Chains: 49
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.68
Source: Enterococcus faecalis
Molecule: 16S rRNA; 30S ribosomal protein S3; 30S ribosomal protein S4; 30S ribosomal protein S5…
UniProt: A0A1B4XKR8, A0A1B4XRV7, A0A1B4XKW0, A0A1B4XKB6, A0A1B4XKQ3, A0A1B4XKS6, A0A1B4XSA2, A0A1B4XKR5, A0A1B4XKV1, A0A1B4XKQ7, A0A1B4XKT7, A0A1B4XKT0, A0A1B4XRW3, A0A1B4XP69, A0A1B4XKS3, A0A1B4XKB3, A0A1B4XKS0, A0A1B4XQJ7, A0A1B4XKR6, A0A1B4XKR3, A0A1B4XKU7, A0A1B4XKS2, A0A1B4XKU3, A0A1B4XSB2, A0A1B4XKS1, A0A1B4XKT1, A0A1B4XKU1, A0A1B4XKX1, A0A1B4XKS7, A0A1B4XPL8, A0A1B4XM76, A0A1B4XMC1, A0A1B4XKT6, A0A1B4XKR7, A0A1B4XKV5, A0A1X3AL36, A0A1B4XMB1, A0A1B4XRZ8, A0A1B4XKV0, A0A1B4XKW1, A0A1B4XMV6, A0A1B4XMM2, A0A1B4XR98, A0A1B4XSI4, A0A1B4XM73, A0A1B4XKT9
Ligands: ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · resolution 3.68 · 49 distinct chains · 23% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	16S rRNA	rna	1528	—	—
c	30S ribosomal protein S3	protein	204	29% helix, 20% strand	A0A1B4XKR8
d	30S ribosomal protein S4	protein	201	33% helix, 6% strand	A0A1B4XRV7
e	30S ribosomal protein S5	protein	163	25% helix, 25% strand	A0A1B4XKW0
f	30S ribosomal protein S6	protein	97	22% helix, 38% strand	A0A1B4XKB6
g	30S ribosomal protein S7	protein	154	53% helix, 4% strand	A0A1B4XKQ3
h	30S ribosomal protein S8	protein	131	26% helix, 26% strand	A0A1B4XKS6
i	30S ribosomal protein S9	protein	128	21% helix, 12% strand	A0A1B4XSA2
j	30S ribosomal protein S10	protein	99	25% helix, 38% strand	A0A1B4XKR5
k	30S ribosomal protein S11	protein	117	25% helix, 22% strand	A0A1B4XKV1
l	30S ribosomal protein S12	protein	136	4% helix, 18% strand	A0A1B4XKQ7
m	30S ribosomal protein S13	protein	112	41% helix, 0% strand	A0A1B4XKT7
n	30S ribosomal protein S14 type Z	protein	60	28% helix, 7% strand	A0A1B4XKT0
o	30S ribosomal protein S15	protein	88	68% helix, 0% strand	A0A1B4XRW3
p	30S ribosomal protein S16	protein	89	28% helix, 27% strand	A0A1B4XP69
q	30S ribosomal protein S17	protein	83	0% helix, 51% strand	A0A1B4XKS3
r	30S ribosomal protein S18	protein	66	38% helix, 3% strand	A0A1B4XKB3
s	30S ribosomal protein S19	protein	78	10% helix, 17% strand	A0A1B4XKS0
t	30S ribosomal protein S20	protein	81	79% helix, 0% strand	A0A1B4XQJ7
A	23S rRNA	rna	2897	—	—
B	5S rRNA	rna	116	—	—
C	50S ribosomal protein L2	protein	275	2% helix, 21% strand	A0A1B4XKR6
D	50S ribosomal protein L3	protein	207	4% helix, 26% strand	A0A1B4XKR3
E	50S ribosomal protein L4	protein	206	29% helix, 9% strand	A0A1B4XKU7
F	50S ribosomal protein L5	protein	176	36% helix, 14% strand	A0A1B4XKS2
G	50S ribosomal protein L6	protein	176	17% helix, 24% strand	A0A1B4XKU3
K	50S ribosomal protein L13	protein	145	21% helix, 12% strand	A0A1B4XSB2
L	50S ribosomal protein L14	protein	122	10% helix, 30% strand	A0A1B4XKS1
M	50S ribosomal protein L15	protein	146	16% helix, 10% strand	A0A1B4XKT1
N	50S ribosomal protein L16	protein	141	16% helix, 18% strand	A0A1B4XKU1
O	50S ribosomal protein L17	protein	123	30% helix, 12% strand	A0A1B4XKX1
P	50S ribosomal protein L18	protein	117	32% helix, 11% strand	A0A1B4XKS7
Q	50S ribosomal protein L19	protein	114	9% helix, 27% strand	A0A1B4XPL8
R	50S ribosomal protein L20	protein	114	68% helix, 0% strand	A0A1B4XM76
S	50S ribosomal protein L21	protein	102	0% helix, 33% strand	A0A1B4XMC1
T	50S ribosomal protein L22	protein	112	34% helix, 34% strand	A0A1B4XKT6
U	50S ribosomal protein L23	protein	88	13% helix, 23% strand	A0A1B4XKR7
V	50S ribosomal protein L24	protein	101	3% helix, 38% strand	A0A1B4XKV5
W	50S ribosomal protein L25	protein	94	16% helix, 31% strand	A0A1X3AL36
X	50S ribosomal protein L27	protein	76	0% helix, 32% strand	A0A1B4XMB1
Y	50S ribosomal protein L28	protein	54	0% helix, 26% strand	A0A1B4XRZ8
Z	50S ribosomal protein L29	protein	61	72% helix, 0% strand	A0A1B4XKV0
0	50S ribosomal protein L30	protein	58	22% helix, 28% strand	A0A1B4XKW1
1	50S ribosomal protein L31 type B	protein	60	0% helix, 13% strand	A0A1B4XMV6
2	50S ribosomal protein L32	protein	56	13% helix, 14% strand	A0A1B4XMM2
3	50S ribosomal protein L33	protein	49	0% helix, 53% strand	A0A1B4XR98
4	50S ribosomal protein L34	protein	43	21% helix, 0% strand	A0A1B4XSI4
5	50S ribosomal protein L35	protein	64	17% helix, 11% strand	A0A1B4XM73
6	50S ribosomal protein L36	protein	38	0% helix, 32% strand	A0A1B4XKT9

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains n, 2, 3, 6

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	1187	0.87	0.89	91	empty
2	1096	0.87	0.89	99	empty
3	950	0.87	0.89	94	empty
4	749	0.87	0.91	66	empty
5	1061	0.85	0.87	99	empty

Interfaces

101 interfaces between chains.

A–C · 7336 Å² buried · 141 hydrogen bonds · protein-nucleic
A–D · 4979 Å² buried · 75 hydrogen bonds · protein-nucleic
A–M · 4329 Å² buried · 71 hydrogen bonds · protein-nucleic
A–E · 4316 Å² buried · 69 hydrogen bonds · protein-nucleic
A–R · 3660 Å² buried · 59 hydrogen bonds · protein-nucleic

Analyse

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