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70S termination complex with RF2 bound to the UGA codon. Partially rotated ribosome with RF2 bound (Structure III).

Analyse 70S termination complex with RF2 bound to the UGA codon. Partially rotated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6OGF
Type: protein + RNA
Length: 10,768 residues
Chains: 55
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.9
Source: Escherichia coli; SYNTHETIC CONSTRUCT
Molecule: 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal protein L4; 50S…
UniProt: P60422, P60438, D7Z9F6, D7Z9G7, D7Z9H0, D7ZI15, D7ZET0, D7Z9G5, A0A037Y8L6, P0ADY7, B7N179, D7Z9H1, D7ZKU3, B7MAS6, D7ZEN7, D7Z9G0, D7X2Z9, D7Z9G6, D7XH79, P0A7L8, S0YB49, D7Z9G3, D7Z9H3, D7ZGG2, D7Z9P0, B7MGC4, D7Z814, A0A0E2L017, D7ZK99, B7MCS9, D7Z9H7, D7Z9H2, D7ZI17, D7ZAN1, D7Z9G9, D7ZES9, D7Z9F4, B7MCR3, D7ZAN0, H4UQ02, D7Z9G8, D7ZEL4, B7MIU7, D7Z9G4, A0A0E2KXL3, D7Z9F9, D7ZAS2, A0A0E2L2J1, B7MIX0, A0A2S5ZJX2
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · resolution 3.9 · 55 distinct chains · 29% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
b	50S ribosomal protein L2	protein	271	7% helix, 27% strand	P60422
c	50S ribosomal protein L3	protein	209	9% helix, 37% strand	P60438
d	50S ribosomal protein L4	protein	201	32% helix, 10% strand	D7Z9F6
e	50S ribosomal protein L5	protein	177	31% helix, 17% strand	D7Z9G7
f	50S ribosomal protein L6	protein	176	18% helix, 36% strand	D7Z9H0
g	50S ribosomal protein L9	protein	149	28% helix, 15% strand	D7ZI15
j	50S ribosomal protein L13	protein	142	32% helix, 14% strand	D7ZET0
k	50S ribosomal protein L14	protein	122	8% helix, 33% strand	D7Z9G5
l	50S ribosomal protein L15	protein	143	13% helix, 11% strand	A0A037Y8L6
m	50S ribosomal protein L16	protein	136	20% helix, 27% strand	P0ADY7
n	50S ribosomal protein L17	protein	120	45% helix, 15% strand	B7N179
o	50S ribosomal protein L18	protein	116	46% helix, 19% strand	D7Z9H1
p	50S ribosomal protein L19	protein	114	17% helix, 36% strand	D7ZKU3
q	50S ribosomal protein L20	protein	117	74% helix, 0% strand	B7MAS6
r	50S ribosomal protein L21	protein	103	0% helix, 48% strand	D7ZEN7
s	50S ribosomal protein L22	protein	110	37% helix, 38% strand	D7Z9G0
t	50S ribosomal protein L23	protein	93	28% helix, 35% strand	D7X2Z9
u	50S ribosomal protein L24	protein	102	3% helix, 43% strand	D7Z9G6
v	50S ribosomal protein L25	protein	94	22% helix, 43% strand	D7XH79
w	50S ribosomal protein L27	protein	75	0% helix, 40% strand	P0A7L8
x	50S ribosomal protein L28	protein	77	25% helix, 29% strand	S0YB49
y	50S ribosomal protein L29	protein	63	79% helix, 0% strand	D7Z9G3
z	50S ribosomal protein L30	protein	58	33% helix, 26% strand	D7Z9H3
B	50S ribosomal protein L32	protein	56	18% helix, 16% strand	D7ZGG2
C	50S ribosomal protein L33	protein	50	0% helix, 50% strand	D7Z9P0
D	50S ribosomal protein L34	protein	46	50% helix, 0% strand	B7MGC4
E	50S ribosomal protein L35	protein	64	27% helix, 11% strand	D7Z814
F	50S ribosomal protein L36	protein	38	8% helix, 32% strand	A0A0E2L017
G	30S ribosomal protein S2	protein	225	41% helix, 8% strand	D7ZK99
H	30S ribosomal protein S3	protein	206	37% helix, 29% strand	B7MCS9
I	30S ribosomal protein S4	protein	205	38% helix, 9% strand	D7Z9H7
J	30S ribosomal protein S5	protein	157	27% helix, 25% strand	D7Z9H2
K	30S ribosomal protein S6	protein	101	27% helix, 23% strand	D7ZI17
L	30S ribosomal protein S7	protein	151	53% helix, 5% strand	D7ZAN1
M	30S ribosomal protein S8	protein	129	27% helix, 22% strand	D7Z9G9
N	30S ribosomal protein S9	protein	127	24% helix, 18% strand	D7ZES9
O	30S ribosomal protein S10	protein	98	18% helix, 31% strand	D7Z9F4
P	30S ribosomal protein S11	protein	116	26% helix, 24% strand	B7MCR3
Q	30S ribosomal protein S12	protein	123	7% helix, 26% strand	D7ZAN0
R	30S ribosomal protein S13	protein	114	46% helix, 4% strand	H4UQ02
S	30S ribosomal protein S14	protein	100	37% helix, 3% strand	D7Z9G8
T	30S ribosomal protein S15	protein	88	74% helix, 0% strand	D7ZEL4
U	30S ribosomal protein S16	protein	82	21% helix, 32% strand	B7MIU7
V	30S ribosomal protein S17	protein	80	0% helix, 50% strand	D7Z9G4
W	30S ribosomal protein S18	protein	65	38% helix, 3% strand	A0A0E2KXL3
X	30S ribosomal protein S19	protein	79	19% helix, 11% strand	D7Z9F9
Y	30S ribosomal protein S20	protein	85	82% helix, 0% strand	D7ZAS2
Z	30S ribosomal protein S21	protein	65	35% helix, 3% strand	A0A0E2L2J1
a	50S ribosomal protein L1	protein	134	25% helix, 21% strand	B7MIX0
3	16S ribosomal RNA	rna	1539	—	—
1	23S ribosomal RNA	rna	2903	—	—
2	5S ribosomal RNA	rna	120	—	—
5	tRNAfMet	rna	73	—	—
4	mRNA	rna	20	—	—
8	Peptide chain release factor 2	protein	361	46% helix, 17% strand	A0A2S5ZJX2

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	1015	0.87	0.89	84	empty
2	1050	0.87	0.89	113	empty
3	989	0.87	0.89	90	empty
4	829	0.87	0.91	87	empty
5	750	0.87	0.91	81	empty

Interfaces

126 interfaces between chains.

b–1 · 7105 Å² buried · 143 hydrogen bonds · protein-nucleic
c–1 · 5179 Å² buried · 122 hydrogen bonds · protein-nucleic
l–1 · 4619 Å² buried · 95 hydrogen bonds · protein-nucleic
q–1 · 4292 Å² buried · 103 hydrogen bonds · protein-nucleic
d–1 · 4274 Å² buried · 83 hydrogen bonds · protein-nucleic

Compared structures

B7MAS6 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L20 (B7MAS6) · a predicted model of the same protein · chain q against A, TM-score 0.98
B7N179 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L17 (B7N179) · a predicted model of the same protein · chain n against A, TM-score 0.98
B7MCS9 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S3 (B7MCS9) · a predicted model of the same protein · chain H against A, TM-score 0.97
B7MCR3 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S11 (B7MCR3) · a predicted model of the same protein · chain P against A, TM-score 0.93
B7MIU7 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S16 (B7MIU7) · a predicted model of the same protein · chain U against A, TM-score 0.93
B7MGC4 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L34 (B7MGC4) · a predicted model of the same protein · chain D against A, TM-score 0.90
B7MIX0 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L1 (B7MIX0) · a predicted model of the same protein · chain a against A, TM-score 0.86

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