Research workbench

Non-rotated ribosome (Structure I)

Analyse Non-rotated ribosome (Structure I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OFX
Type: protein + RNA
Length: 10,411 residues
Chains: 54
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.3
Source: Escherichia coli; Escherichia coli (strain K12); Escherichia coli K-12…
Molecule: 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal protein L4; 50S…
UniProt: P60422, P60438, P60723, P62399, P0AG55, P0A7R1, P0AA10, P0ADY3, P02413, P0ADY7, P0AG44, P0C018, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P68919, P0A7L8, P0A7M2, P0A7M6, P0AG51, P0A7N4, P0A7N9, P0A7P5, P0A7Q1, P0A7Q6, P0A7V0, P0A7V3, P0A7V8, P0A7W1, P02358, P02359, P0A7W7, P0A7X3, P0A7R5, P0A7R9, P0A7S3, P0A7S9, P0AG59, P0ADZ4, P0A7T3, P0AG63, P0A7T7, P0A7U3, P0A7U7, P68679, P0A7L0
Ligands: FME
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · resolution 3.3 · 54 distinct chains · 29% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
b	50S ribosomal protein L2	protein	271	8% helix, 28% strand	P60422
c	50S ribosomal protein L3	protein	209	11% helix, 36% strand	P60438
d	50S ribosomal protein L4	protein	201	34% helix, 8% strand	P60723
e	50S ribosomal protein L5	protein	177	34% helix, 20% strand	P62399
f	50S ribosomal protein L6	protein	176	19% helix, 30% strand	P0AG55
g	50S ribosomal protein L9	protein	149	30% helix, 19% strand	P0A7R1
j	50S ribosomal protein L13	protein	142	33% helix, 20% strand	P0AA10
k	50S ribosomal protein L14	protein	122	10% helix, 35% strand	P0ADY3
l	50S ribosomal protein L15	protein	143	16% helix, 12% strand	P02413
m	50S ribosomal protein L16	protein	136	21% helix, 28% strand	P0ADY7
n	50S ribosomal protein L17	protein	120	44% helix, 17% strand	P0AG44
o	50S ribosomal protein L18	protein	116	41% helix, 19% strand	P0C018
p	50S ribosomal protein L19	protein	114	18% helix, 39% strand	P0A7K6
q	50S ribosomal protein L20	protein	117	78% helix, 0% strand	P0A7L3
r	50S ribosomal protein L21	protein	103	0% helix, 52% strand	P0AG48
s	50S ribosomal protein L22	protein	110	35% helix, 38% strand	P61175
t	50S ribosomal protein L23	protein	93	30% helix, 33% strand	P0ADZ0
u	50S ribosomal protein L24	protein	102	3% helix, 43% strand	P60624
v	50S ribosomal protein L25	protein	94	22% helix, 44% strand	P68919
w	50S ribosomal protein L27	protein	75	0% helix, 40% strand	P0A7L8
x	50S ribosomal protein L28	protein	77	25% helix, 29% strand	P0A7M2
y	50S ribosomal protein L29	protein	63	71% helix, 0% strand	P0A7M6
z	50S ribosomal protein L30	protein	58	33% helix, 26% strand	P0AG51
B	50S ribosomal protein L32	protein	56	18% helix, 16% strand	P0A7N4
C	50S ribosomal protein L33	protein	50	0% helix, 56% strand	P0A7N9
D	50S ribosomal protein L34	protein	46	57% helix, 0% strand	P0A7P5
E	50S ribosomal protein L35	protein	64	27% helix, 11% strand	P0A7Q1
F	50S ribosomal protein L36	protein	38	8% helix, 45% strand	P0A7Q6
G	30S ribosomal protein S2	protein	225	43% helix, 10% strand	P0A7V0
H	30S ribosomal protein S3	protein	206	39% helix, 27% strand	P0A7V3
I	30S ribosomal protein S4	protein	205	40% helix, 9% strand	P0A7V8
J	30S ribosomal protein S5	protein	157	26% helix, 25% strand	P0A7W1
K	30S ribosomal protein S6	protein	101	30% helix, 17% strand	P02358
L	30S ribosomal protein S7	protein	151	55% helix, 8% strand	P02359
M	30S ribosomal protein S8	protein	129	28% helix, 23% strand	P0A7W7
N	30S ribosomal protein S9	protein	127	24% helix, 17% strand	P0A7X3
O	30S ribosomal protein S10	protein	98	20% helix, 32% strand	P0A7R5
P	30S ribosomal protein S11	protein	116	20% helix, 28% strand	P0A7R9
Q	30S ribosomal protein S12	protein	123	5% helix, 24% strand	P0A7S3
R	30S ribosomal protein S13	protein	114	47% helix, 2% strand	P0A7S9
S	30S ribosomal protein S14	protein	100	38% helix, 4% strand	P0AG59
T	30S ribosomal protein S15	protein	88	74% helix, 0% strand	P0ADZ4
U	30S ribosomal protein S16	protein	82	22% helix, 34% strand	P0A7T3
V	30S ribosomal protein S17	protein	80	0% helix, 41% strand	P0AG63
W	30S ribosomal protein S18	protein	65	38% helix, 3% strand	P0A7T7
X	30S ribosomal protein S19	protein	79	23% helix, 18% strand	P0A7U3
Y	30S ribosomal protein S20	protein	85	85% helix, 0% strand	P0A7U7
Z	30S ribosomal protein S21	protein	65	46% helix, 3% strand	P68679
a	50S ribosomal protein L1	protein	134	22% helix, 28% strand	P0A7L0
3	16S ribosomal RNA	rna	1539	—	—
1	23S ribosomal RNA	rna	2903	—	—
2	5S ribosomal RNA	rna	120	—	—
5	tRNAfMet	rna	77	—	—
4	mRNA	rna	20	—	—

Ligands and binding sites

FME · N-formylmethionine · ligand · chains 1, 5

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	1139	0.88	0.90	104	empty
2	1028	0.88	0.90	107	empty
3	1124	0.88	0.90	114	empty
4	977	0.88	0.90	95	empty
5	781	0.87	0.91	68	empty

Interfaces

123 interfaces between chains.

b–1 · 7276 Å² buried · 169 hydrogen bonds · protein-nucleic
c–1 · 5102 Å² buried · 116 hydrogen bonds · protein-nucleic
l–1 · 4608 Å² buried · 91 hydrogen bonds · protein-nucleic
d–1 · 4299 Å² buried · 86 hydrogen bonds · protein-nucleic
q–1 · 4240 Å² buried · 109 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

P0AG48 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L21 (P0AG48) · a predicted model of the same protein · chain r against A, TM-score 0.93
P0A7L0 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L1 (P0A7L0) · a predicted model of the same protein · chain a against A, TM-score 0.87

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