MolNFT v1 · #184414 · protein + RNA

Rqch dr variant bound to 50S-peptidyl-tRNA-rqcp rqc complex (rigid body refinement)

7OPE · 23S rRNA: “Rqch dr variant bound to 50S-peptidyl-tRNA-rqcp rqc complex (rigid body refinement)”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #184414 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 7OPE
Type: protein + RNA
Length: 6,814 residues
Chains: 33
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S rRNA; 5S rRNA; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal…
UniProt: P42919, P42920, P42921, P12877, P46898, Q06796, P42923, P70974, P12875, P19946, P14577, P20277, P46899, O31742, P55873, P26908, P42060, P42924, P0CI78, P05657, P37807, P12873, P19947, O34687, P56849, P05647, P55874, P20278, P37557, A0A6M4JI41
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 33 distinct chains · 28% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S rRNA	rna	2814	—	—
B	5S rRNA	rna	112	—	—
E	50S ribosomal protein L2	protein	272	2% helix, 25% strand	P42919
F	50S ribosomal protein L3	protein	206	8% helix, 38% strand	P42920
G	50S ribosomal protein L4	protein	205	32% helix, 15% strand	P42921
H	50S ribosomal protein L5	protein	176	41% helix, 22% strand	P12877
I	50S ribosomal protein L6	protein	175	19% helix, 30% strand	P46898
K	50S ribosomal protein L11	protein	132	42% helix, 20% strand	Q06796
L	50S ribosomal protein L10	protein	113	53% helix, 19% strand	P42923
N	50S ribosomal protein L13	protein	142	32% helix, 19% strand	P70974
O	50S ribosomal protein L14	protein	122	7% helix, 39% strand	P12875
P	50S ribosomal protein L15	protein	146	17% helix, 12% strand	P19946
Q	50S ribosomal protein L16	protein	135	21% helix, 25% strand	P14577
R	50S ribosomal protein L17	protein	119	50% helix, 19% strand	P20277
S	50S ribosomal protein L18	protein	120	35% helix, 21% strand	P46899
T	50S ribosomal protein L19	protein	115	10% helix, 43% strand	O31742
U	50S ribosomal protein L20	protein	117	79% helix, 0% strand	P55873
V	50S ribosomal protein L21	protein	100	0% helix, 48% strand	P26908
W	50S ribosomal protein L22	protein	109	39% helix, 37% strand	P42060
X	50S ribosomal protein L23	protein	90	27% helix, 28% strand	P42924
Y	50S ribosomal protein L24	protein	101	3% helix, 42% strand	P0CI78
2	TRNA-ala-ugc	rna	70	—	—
a	50S ribosomal protein L27	protein	81	0% helix, 36% strand	P05657
b	50S ribosomal protein L28	protein	58	12% helix, 38% strand	P37807
c	50S ribosomal protein L29	protein	65	80% helix, 0% strand	P12873
d	50S ribosomal protein L30	protein	58	34% helix, 26% strand	P19947
f	50S ribosomal protein L32	protein	53	13% helix, 23% strand	O34687
g	50S ribosomal protein L33 1	protein	48	0% helix, 54% strand	P56849
h	50S ribosomal protein L34	protein	44	57% helix, 0% strand	P05647
i	50S ribosomal protein L35	protein	64	38% helix, 14% strand	P55874
j	50S ribosomal protein L36	protein	37	8% helix, 38% strand	P20278
1	Uncharacterized protein yabo	protein	83	27% helix, 31% strand	P37557
0	RQC2 homolog rqch	protein	532	37% helix, 23% strand	A0A6M4JI41

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	1004	0.89	0.91	102	empty
2	1062	0.86	0.88	92	empty
3	746	0.85	0.90	85	empty
4	664	0.85	0.90	78	empty
5	464	0.84	0.92	62	empty

Interfaces

67 interfaces between chains.

A–E · 7282 Å² buried · 175 hydrogen bonds · protein-nucleic
A–F · 5031 Å² buried · 125 hydrogen bonds · protein-nucleic
A–P · 4537 Å² buried · 104 hydrogen bonds · protein-nucleic
A–G · 4411 Å² buried · 95 hydrogen bonds · protein-nucleic
A–U · 4041 Å² buried · 81 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

7OPE · RqcH DR variant bound to 50S-peptidyl-tRNA-RqcP RQC complex (rigid body refinement) · the same entry in another collection · chain O against O, 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 P42923
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 O31742
Every structure of UniProt P55873
Every structure of UniProt P26908
Every structure of UniProt P42060
Every structure of UniProt P42924
Every structure of UniProt P0CI78
Every structure of UniProt P05657
Every structure of UniProt P37807
Every structure of UniProt P12873
Every structure of UniProt P19947
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 P37557
Every structure of UniProt A0A6M4JI41
Elsewhere: RCSB PDB 7OPE · PDBe 7OPE · UniProt P42919 · UniProt P42920 · UniProt P42921 · UniProt P12877 · UniProt P46898 · UniProt Q06796 · UniProt P42923 · UniProt P70974 · UniProt P12875 · UniProt P19946 · UniProt P14577 · UniProt P20277 · UniProt P46899 · UniProt O31742 · UniProt P55873 · UniProt P26908 · UniProt P42060 · UniProt P42924 · UniProt P0CI78 · UniProt P05657 · UniProt P37807 · UniProt P12873 · UniProt P19947 · UniProt O34687 · UniProt P56849 · UniProt P05647 · UniProt P55874 · UniProt P20278 · UniProt P37557 · UniProt A0A6M4JI41

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