Research workbench

Ribosomal methyltransferase ksga bound to small ribosomal subunit

Analyse Ribosomal methyltransferase ksga bound to small ribosomal subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7O5H
Type: protein + RNA
Length: 2,694 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribosomal RNA small subunit methyltransferase a; 16S rRNA; 30S ribosomal protein S2; 30S…
EC: 2.1.1.182
UniProt: A0A4S5B3V1, A0A3K3SDJ5, V0YKB3, A1AGJ2, P02358, H4JDM0, A0A5I5F5V9, I2UHF1, E9YUR8, C3SYP2, T6LV72, A7ZV73, I4T5W9, A0A5C9AJ78
Ligands: MG
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 15 distinct chains · 40% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
V	Ribosomal RNA small subunit methyltransferase a (EC 2.1.1.182)	protein	251	41% helix, 20% strand	A0A4S5B3V1
A	16S rRNA	rna	964	—	—
B	30S ribosomal protein S2	protein	225	53% helix, 14% strand	A0A3K3SDJ5
D	30S ribosomal protein S4	protein	205	46% helix, 10% strand	V0YKB3
E	30S ribosomal protein S5	protein	158	31% helix, 35% strand	A1AGJ2
F	30S ribosomal protein S6, fully modified isoform	protein	103	31% helix, 47% strand	P02358
H	30S ribosomal protein S8	protein	129	32% helix, 29% strand	H4JDM0
K	30S ribosomal protein S11	protein	117	26% helix, 30% strand	A0A5I5F5V9
L	30S ribosomal protein S12	protein	123	7% helix, 25% strand	I2UHF1
O	30S ribosomal protein S15	protein	87	77% helix, 0% strand	E9YUR8
P	30S ribosomal protein S16	protein	82	27% helix, 33% strand	C3SYP2
Q	30S ribosomal protein S17	protein	79	4% helix, 56% strand	T6LV72
R	30S ribosomal protein S18	protein	55	45% helix, 4% strand	A7ZV73
T	30S ribosomal protein S20	protein	86	87% helix, 0% strand	I4T5W9
U	30S ribosomal protein S21	protein	30	70% helix, 3% strand	A0A5C9AJ78

Ligands and binding sites

MG · Magnesium ion · metal · 167 copies · chains A, L, T, D, O, E, F, H, K, U

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	689	0.84	0.88	67	MG
2	1044	0.82	0.84	74	MG
3	573	0.82	0.88	73	MG
4	462	0.81	0.90	52	MG
5	683	0.81	0.87	68	MG

Interfaces

23 interfaces between chains.

A–D · 3277 Å² buried · 79 hydrogen bonds · protein-nucleic
A–L · 2860 Å² buried · 72 hydrogen bonds · protein-nucleic
A–P · 2223 Å² buried · 44 hydrogen bonds · protein-nucleic
A–T · 1976 Å² buried · 46 hydrogen bonds · protein-nucleic
A–K · 1881 Å² buried · 43 hydrogen bonds · protein-nucleic

Compared structures

7O5H · Ribosomal methyltransferase KsgA bound to small ribosomal subunit · the same entry in another collection · chain U against U, 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 A0A4S5B3V1
Every structure of UniProt A0A3K3SDJ5
Every structure of UniProt V0YKB3
Every structure of UniProt A1AGJ2
Every structure of UniProt P02358
Every structure of UniProt H4JDM0
Every structure of UniProt A0A5I5F5V9
Every structure of UniProt I2UHF1
Every structure of UniProt E9YUR8
Every structure of UniProt C3SYP2
Every structure of UniProt T6LV72
Every structure of UniProt A7ZV73
Every structure of UniProt I4T5W9
Every structure of UniProt A0A5C9AJ78
Elsewhere: RCSB PDB 7O5H · PDBe 7O5H · UniProt A0A4S5B3V1 · UniProt A0A3K3SDJ5 · UniProt V0YKB3 · UniProt A1AGJ2 · UniProt P02358 · UniProt H4JDM0 · UniProt A0A5I5F5V9 · UniProt I2UHF1 · UniProt E9YUR8 · UniProt C3SYP2 · UniProt T6LV72 · UniProt A7ZV73 · UniProt I4T5W9 · UniProt A0A5C9AJ78

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