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Cryo-EM structure of nusg-ctd bound to 70S ribosome (30S: nusg-ctd fragment)

Analyse Cryo-EM structure of nusg-ctd bound to 70S ribosome (30S: nusg-ctd fragment) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6XE0
Type: protein + RNA
Length: 3,952 residues
Chains: 22
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal protein S4; 30S…
UniProt: P0A7V0, P0A7V3, P0A7V8, P0A7W1, P02358, P02359, P0A7W7, P0A7X3, P0A7R5, P0A7R9, P0A7S3, P0A7S9, P0AG59, P0ADZ4, P0A7T3, P0AG63, P0A7T7, P0A7U3, P0A7U7, P68679, P0AFG0
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 22 distinct chains · 34% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	30S ribosomal protein S2	protein	218	40% helix, 9% strand	P0A7V0
B	30S ribosomal protein S3	protein	206	37% helix, 29% strand	P0A7V3
C	30S ribosomal protein S4	protein	205	41% helix, 10% strand	P0A7V8
D	30S ribosomal protein S5	protein	150	21% helix, 35% strand	P0A7W1
E	30S ribosomal protein S6	protein	100	27% helix, 28% strand	P02358
F	30S ribosomal protein S7	protein	151	56% helix, 5% strand	P02359
G	30S ribosomal protein S8	protein	129	31% helix, 30% strand	P0A7W7
H	30S ribosomal protein S9	protein	127	27% helix, 18% strand	P0A7X3
I	30S ribosomal protein S10	protein	98	20% helix, 38% strand	P0A7R5
J	30S ribosomal protein S11	protein	117	27% helix, 29% strand	P0A7R9
K	30S ribosomal protein S12	protein	123	7% helix, 26% strand	P0A7S3
L	30S ribosomal protein S13	protein	114	46% helix, 2% strand	P0A7S9
M	30S ribosomal protein S14	protein	96	36% helix, 6% strand	P0AG59
O	30S ribosomal protein S15	protein	88	73% helix, 0% strand	P0ADZ4
P	30S ribosomal protein S16	protein	82	23% helix, 20% strand	P0A7T3
Q	30S ribosomal protein S17	protein	80	0% helix, 63% strand	P0AG63
R	30S ribosomal protein S18	protein	55	45% helix, 4% strand	P0A7T7
S	30S ribosomal protein S19	protein	79	25% helix, 14% strand	P0A7U3
T	30S ribosomal protein S20	protein	85	84% helix, 0% strand	P0A7U7
U	30S ribosomal protein S21	protein	51	31% helix, 0% strand	P68679
V	Transcription TERMINATION/ANTITERMINATION protein nusg	protein	59	0% helix, 41% strand	P0AFG0
W	16S rRNA	rna	1539	—	—

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	667	0.86	0.91	82	empty
2	857	0.85	0.88	74	empty
3	1128	0.85	0.87	70	empty
4	1045	0.85	0.86	92	empty
5	823	0.84	0.88	63	empty

Interfaces

42 interfaces between chains.

C–W · 3489 Å² buried · 92 hydrogen bonds · protein-nucleic
H–W · 3181 Å² buried · 80 hydrogen bonds · protein-nucleic
K–W · 3036 Å² buried · 80 hydrogen bonds · protein-nucleic
M–W · 2493 Å² buried · 67 hydrogen bonds · protein-nucleic
T–W · 2405 Å² buried · 56 hydrogen bonds · protein-nucleic

Compared structures

6XE0 · Cryo-EM structure of NusG-CTD bound to 70S ribosome (30S: NusG-CTD fragment) · the same entry in another collection · chain W against W, 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 P0A7V0
Every structure of UniProt P0A7V3
Every structure of UniProt P0A7V8
Every structure of UniProt P0A7W1
Every structure of UniProt P02358
Every structure of UniProt P02359
Every structure of UniProt P0A7W7
Every structure of UniProt P0A7X3
Every structure of UniProt P0A7R5
Every structure of UniProt P0A7R9
Every structure of UniProt P0A7S3
Every structure of UniProt P0A7S9
Every structure of UniProt P0AG59
Every structure of UniProt P0ADZ4
Every structure of UniProt P0A7T3
Every structure of UniProt P0AG63
Every structure of UniProt P0A7T7
Every structure of UniProt P0A7U3
Every structure of UniProt P0A7U7
Every structure of UniProt P68679
Every structure of UniProt P0AFG0
Elsewhere: RCSB PDB 6XE0 · PDBe 6XE0 · UniProt P0A7V0 · UniProt P0A7V3 · UniProt P0A7V8 · UniProt P0A7W1 · UniProt P02358 · UniProt P02359 · UniProt P0A7W7 · UniProt P0A7X3 · UniProt P0A7R5 · UniProt P0A7R9 · UniProt P0A7S3 · UniProt P0A7S9 · UniProt P0AG59 · UniProt P0ADZ4 · UniProt P0A7T3 · UniProt P0AG63 · UniProt P0A7T7 · UniProt P0A7U3 · UniProt P0A7U7 · UniProt P68679 · UniProt P0AFG0

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