MolNFT v1 · #173147 · protein + RNA

Structure of the bacterial rqc complex (decoding state)

7AQC · 23S ribosomal RNA: “Structure of the bacterial rqc complex (decoding state)”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #173147 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7AQC
Type: protein + RNA
Length: 6,829 residues
Chains: 34
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S ribosomal RNA; 5S ribosomal RNA; 50S ribosomal protein L2; 50S ribosomal protein L3…
UniProt: P42919, P42920, P42921, P12877, P46898, Q06796, P70974, P12875, P19946, P14577, P20277, P46899, P55873, O34693, P42060, P0CI78, P05657, P37807, P37557, P19947, O31742, O34687, P56849, P05647, P55874, P20278, P26908, P42924, P12873
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 34 distinct chains · 26% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S ribosomal RNA	rna	2820	—	—
B	5S ribosomal RNA	rna	112	—	—
C	50S ribosomal protein L2	protein	275	10% helix, 25% strand	P42919
D	50S ribosomal protein L3	protein	207	7% helix, 40% strand	P42920
E	50S ribosomal protein L4	protein	205	32% helix, 12% strand	P42921
F	50S ribosomal protein L5	protein	178	28% helix, 14% strand	P12877
G	50S ribosomal protein L6	protein	175	21% helix, 32% strand	P46898
I	50S ribosomal protein L11	protein	133	37% helix, 14% strand	Q06796
J	50S ribosomal protein L13	protein	142	32% helix, 15% strand	P70974
K	50S ribosomal protein L14	protein	122	7% helix, 39% strand	P12875
L	50S ribosomal protein L15	protein	146	18% helix, 11% strand	P19946
M	50S ribosomal protein L16	protein	138	19% helix, 26% strand	P14577
N	50S ribosomal protein L17	protein	119	49% helix, 21% strand	P20277
O	50S ribosomal protein L18	protein	120	33% helix, 18% strand	P46899
P	Ala-tRNA (P-site)	rna	69	—	—
Q	50S ribosomal protein L20	protein	117	72% helix, 0% strand	P55873
R	RQC2 homolog rqch	protein	558	39% helix, 20% strand	O34693
S	50S ribosomal protein L22	protein	109	37% helix, 30% strand	P42060
T	Ala-tRNA (P-site)	rna	76	—	—
U	50S ribosomal protein L24	protein	100	3% helix, 36% strand	P0CI78
V	50S ribosomal protein L27	protein	82	0% helix, 35% strand	P05657
W	Nascent polyalanine	protein	7	0% helix, 0% strand	—
X	50S ribosomal protein L28	protein	58	0% helix, 24% strand	P37807
Y	Uncharacterized protein yabo	protein	84	23% helix, 19% strand	P37557
Z	50S ribosomal protein L30	protein	58	31% helix, 28% strand	P19947
a	50S ribosomal protein L19	protein	114	16% helix, 41% strand	O31742
b	50S ribosomal protein L32	protein	54	13% helix, 15% strand	O34687
c	50S ribosomal protein L33 1	protein	48	0% helix, 60% strand	P56849
d	50S ribosomal protein L34	protein	44	57% helix, 0% strand	P05647
e	50S ribosomal protein L35	protein	64	31% helix, 11% strand	P55874
f	50S ribosomal protein L36	protein	36	17% helix, 25% strand	P20278
g	50S ribosomal protein L21	protein	101	0% helix, 50% strand	P26908
h	50S ribosomal protein L23	protein	93	25% helix, 38% strand	P42924
i	50S ribosomal protein L29	protein	65	86% helix, 0% strand	P12873

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	756	0.88	0.93	66	empty
2	1006	0.88	0.90	93	empty
3	874	0.88	0.91	79	empty
4	958	0.87	0.90	85	empty
5	940	0.87	0.90	74	empty

Interfaces

70 interfaces between chains.

A–C · 7676 Å² buried · 199 hydrogen bonds · protein-nucleic
A–D · 5133 Å² buried · 116 hydrogen bonds · protein-nucleic
A–L · 4580 Å² buried · 103 hydrogen bonds · protein-nucleic
A–E · 4552 Å² buried · 85 hydrogen bonds · protein-nucleic
A–Q · 4081 Å² buried · 97 hydrogen bonds · protein-nucleic

Compared structures

7AQC · Structure of the bacterial RQC complex (Decoding State) · the same entry in another collection · chain L against L, 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 P42919
Every structure of UniProt P42920
Every structure of UniProt P42921
Every structure of UniProt P12877
Every structure of UniProt P46898
Every structure of UniProt Q06796
Every structure of UniProt P70974
Every structure of UniProt P12875
Every structure of UniProt P19946
Every structure of UniProt P14577
Every structure of UniProt P20277
Every structure of UniProt P46899
Every structure of UniProt P55873
Every structure of UniProt O34693
Every structure of UniProt P42060
Every structure of UniProt P0CI78
Every structure of UniProt P05657
Every structure of UniProt P37807
Every structure of UniProt P37557
Every structure of UniProt P19947
Every structure of UniProt O31742
Every structure of UniProt O34687
Every structure of UniProt P56849
Every structure of UniProt P05647
Every structure of UniProt P55874
Every structure of UniProt P20278
Every structure of UniProt P26908
Every structure of UniProt P42924
Every structure of UniProt P12873
Elsewhere: RCSB PDB 7AQC · PDBe 7AQC · UniProt P42919 · UniProt P42920 · UniProt P42921 · UniProt P12877 · UniProt P46898 · UniProt Q06796 · UniProt P70974 · UniProt P12875 · UniProt P19946 · UniProt P14577 · UniProt P20277 · UniProt P46899 · UniProt P55873 · UniProt O34693 · UniProt P42060 · UniProt P0CI78 · UniProt P05657 · UniProt P37807 · UniProt P37557 · UniProt P19947 · UniProt O31742 · UniProt O34687 · UniProt P56849 · UniProt P05647 · UniProt P55874 · UniProt P20278 · UniProt P26908 · UniProt P42924 · UniProt P12873

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