MolNFT v2 · #125623 · protein + RNA

Cryo-EM structure of stringent response factor RelA bound to ErmCL-stalled ribosome complex

5L3P · 23S ribosomal RNA: “Cryo-EM structure of stringent response factor RelA bound to ErmCL-stalled ribosome complex”. Electron microscopy at 3.7, 20 pockets (best druggability 0.87). MolNFT v2 #125623 on GenesisL1: 3D structure, binding…

PDB: 5L3P
Type: protein + RNA
Length: 11,199 residues
Chains: 58
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.7
Source: Escherichia coli; Escherichia coli (strain K12); Escherichia coli K-12…
Molecule: 23S ribosomal RNA; 5S ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal protein L3…
EC: 2.7.6.5
UniProt: P60422, P60438, P60723, P62399, P0AG55, P0A7R1, P0AA10, P0ADY3, P02413, P0ADY7, P0AG44, P0C018, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P68919, P0A7L8, P0A7M2, P0A7M6, P0AG51, P0A7M9, P0A7N4, P0A7N9, P0A7P5, P0A7Q1, P0A7Q6, P0A7V0, P0A7V3, P0A7V8, P0A7W1, P02358, P02359, P0A7W7, P0A7X3, P0A7R5, P0A7R9, P0A7S3, P0A7S9, P0ADZ4, P0A7T3, P0AG63, P0A7T7, P0A7U7, P68679, P0A7J3, P0A7J7, P0AG59, P0A7U3, P0AG22
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · resolution 3.7 · 58 distinct chains · 32% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S ribosomal RNA	rna	2890	—	—
B	5S ribosomal RNA	rna	120	—	—
D	50S ribosomal protein L2	protein	271	6% helix, 25% strand	P60422
E	50S ribosomal protein L3	protein	209	9% helix, 24% strand	P60438
F	50S ribosomal protein L4	protein	201	35% helix, 6% strand	P60723
G	50S ribosomal protein L5	protein	177	36% helix, 11% strand	P62399
H	50S ribosomal protein L6	protein	176	19% helix, 25% strand	P0AG55
I	50S ribosomal protein L9	protein	149	36% helix, 13% strand	P0A7R1
N	50S ribosomal protein L13	protein	142	33% helix, 13% strand	P0AA10
O	50S ribosomal protein L14	protein	122	9% helix, 34% strand	P0ADY3
P	50S ribosomal protein L15	protein	143	24% helix, 8% strand	P02413
Q	50S ribosomal protein L16	protein	136	21% helix, 22% strand	P0ADY7
R	50S ribosomal protein L17	protein	120	43% helix, 16% strand	P0AG44
S	50S ribosomal protein L18	protein	116	42% helix, 12% strand	P0C018
T	50S ribosomal protein L19	protein	114	18% helix, 35% strand	P0A7K6
U	50S ribosomal protein L20	protein	117	79% helix, 0% strand	P0A7L3
V	50S ribosomal protein L21	protein	103	0% helix, 44% strand	P0AG48
W	50S ribosomal protein L22	protein	110	40% helix, 27% strand	P61175
X	50S ribosomal protein L23	protein	93	31% helix, 23% strand	P0ADZ0
Y	50S ribosomal protein L24	protein	102	3% helix, 26% strand	P60624
Z	50S ribosomal protein L25	protein	94	20% helix, 40% strand	P68919
0	50S ribosomal protein L27	protein	75	0% helix, 31% strand	P0A7L8
1	50S ribosomal protein L28	protein	77	25% helix, 26% strand	P0A7M2
2	50S ribosomal protein L29	protein	63	71% helix, 0% strand	P0A7M6
3	50S ribosomal protein L30	protein	58	38% helix, 21% strand	P0AG51
4	50S ribosomal protein L31	protein	66	27% helix, 20% strand	P0A7M9
5	50S ribosomal protein L32	protein	56	18% helix, 11% strand	P0A7N4
6	50S ribosomal protein L33	protein	50	0% helix, 24% strand	P0A7N9
7	50S ribosomal protein L34	protein	46	50% helix, 0% strand	P0A7P5
8	50S ribosomal protein L35	protein	64	25% helix, 9% strand	P0A7Q1
9	50S ribosomal protein L36	protein	38	8% helix, 32% strand	P0A7Q6
a	16S ribosomal RNA	rna	1539	—	—
b	30S ribosomal protein S2	protein	218	43% helix, 7% strand	P0A7V0
c	30S ribosomal protein S3	protein	206	41% helix, 22% strand	P0A7V3
d	30S ribosomal protein S4	protein	205	39% helix, 6% strand	P0A7V8
e	30S ribosomal protein S5	protein	157	28% helix, 17% strand	P0A7W1
f	30S ribosomal protein S6	protein	100	31% helix, 22% strand	P02358
g	30S ribosomal protein S7	protein	151	52% helix, 7% strand	P02359
h	30S ribosomal protein S8	protein	129	28% helix, 17% strand	P0A7W7
i	30S ribosomal protein S9	protein	127	25% helix, 17% strand	P0A7X3
j	30S ribosomal protein S10	protein	98	21% helix, 28% strand	P0A7R5
k	30S ribosomal protein S11	protein	116	22% helix, 28% strand	P0A7R9
l	30S ribosomal protein S12	protein	123	7% helix, 20% strand	P0A7S3
m	30S ribosomal protein S13	protein	114	48% helix, 2% strand	P0A7S9
o	30S ribosomal protein S15	protein	88	69% helix, 0% strand	P0ADZ4
p	30S ribosomal protein S16	protein	82	24% helix, 20% strand	P0A7T3
q	30S ribosomal protein S17	protein	80	0% helix, 43% strand	P0AG63
r	30S ribosomal protein S18	protein	65	48% helix, 3% strand	P0A7T7
t	30S ribosomal protein S20	protein	85	78% helix, 0% strand	P0A7U7
u	30S ribosomal protein S21	protein	65	49% helix, 2% strand	P68679
v	mRNA	rna	6	—	—
x	P-site tRNA	rna	77	—	—
J	50S ribosomal protein L10	protein	131	40% helix, 0% strand	P0A7J3
K	50S ribosomal protein L11	protein	141	28% helix, 3% strand	P0A7J7
n	30S ribosomal protein S14	protein	101	47% helix, 1% strand	P0AG59
s	30S ribosomal protein S19	protein	79	25% helix, 10% strand	P0A7U3
z	GTP pyrophosphokinase,GTP pyrophosphokinase,GTP pyrophosphokinase (EC 2.7.6.5)	protein	545	54% helix, 14% strand	P0AG22
y	deacylated A/R-tRNA	rna	73	—	—

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	943	0.87	0.90	92	empty
2	1153	0.87	0.90	106	empty
3	742	0.87	0.91	84	empty
4	588	0.86	0.93	50	empty
5	720	0.86	0.90	88	empty

Interfaces

133 interfaces between chains.

A–D · 7575 Å² buried · 159 hydrogen bonds · protein-nucleic
A–E · 5209 Å² buried · 110 hydrogen bonds · protein-nucleic
A–P · 4610 Å² buried · 96 hydrogen bonds · protein-nucleic
A–F · 4254 Å² buried · 81 hydrogen bonds · protein-nucleic
A–U · 4214 Å² buried · 91 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 46 modified, 1 disulfide (nucleotide modification, disulfide).

Compared structures

P60422 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L2 (P60422) · a predicted model of the same protein · chain D against A, TM-score 0.98
P0ADY7 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L16 (P0ADY7) · a predicted model of the same protein · chain Q against A, TM-score 0.98
P0A7V3 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S3 (P0A7V3) · a predicted model of the same protein · chain c against A, TM-score 0.97
P0A7L3 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L20 (P0A7L3) · a predicted model of the same protein · chain U against A, TM-score 0.97
P0AA10 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L13 (P0AA10) · a predicted model of the same protein · chain N against A, TM-score 0.97
P0A7K6 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L19 (P0A7K6) · a predicted model of the same protein · chain T against A, TM-score 0.97
P0A7W7 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S8 (P0A7W7) · a predicted model of the same protein · chain h against A, TM-score 0.97
P68919 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L25 (P68919) · a predicted model of the same protein · chain Z against A, TM-score 0.96
P0AG55 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L6 (P0AG55) · a predicted model of the same protein · chain H against A, TM-score 0.96
P0C018 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L18 (P0C018) · a predicted model of the same protein · chain S against A, TM-score 0.96
P0A7V8 · AlphaFold monomer V2.0 prediction for 30S ribosomal protein S4 (P0A7V8) · a predicted model of the same protein · chain d against A, TM-score 0.96
P0A7L8 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L27 (P0A7L8) · a predicted model of the same protein · chain 0 against A, TM-score 0.96

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