MolNFT v1 · #163968 · protein + RNA

Cryo-EM structure of 50S-rsfs complex from staphylococcus aureus

6SJ6 · 23S ribosomal RNA: “Cryo-EM structure of 50S-rsfs complex from staphylococcus aureus”. Electron microscopy, 2 ligands (MG, K), 20 pockets (best druggability 0.88). MolNFT v1 #163968 on GenesisL1: 3D structure, binding sites and…

PDB: 6SJ6
Type: protein + RNA
Length: 5,308 residues
Chains: 26
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: P60430, Q2FW06, Q2FW07, Q2FW38, Q2FW16, P0A0F8, Q2FW13, Q2FW33, Q2FW22, Q2FZ42, Q2FXQ1, Q2FXS8, Q2FW11, Q2FW08, Q2FW17, Q2G0S0, Q2FXT0, Q2FZ60, Q2FW14, P0A0G2, Q2FZF1, Q2FUQ0, Q2FXQ0, Q2G298
Ligands: MG, K
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 26 distinct chains · 16% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S ribosomal RNA	rna	2585	—	—
B	5S ribosomal RNA	rna	112	—	—
D	50S ribosomal protein L2	protein	242	3% helix, 26% strand	P60430
E	50S ribosomal protein L3	protein	216	6% helix, 36% strand	Q2FW06
F	50S ribosomal protein L4	protein	203	18% helix, 7% strand	Q2FW07
M	50S ribosomal protein L13	protein	145	14% helix, 12% strand	Q2FW38
N	50S ribosomal protein L14	protein	122	6% helix, 35% strand	Q2FW16
O	50S ribosomal protein L15	protein	146	11% helix, 10% strand	P0A0F8
P	50S ribosomal protein L16	protein	137	18% helix, 18% strand	Q2FW13
Q	50S ribosomal protein L17	protein	121	39% helix, 17% strand	Q2FW33
R	50S ribosomal protein L18	protein	112	20% helix, 8% strand	Q2FW22
S	50S ribosomal protein L19	protein	103	4% helix, 32% strand	Q2FZ42
T	50S ribosomal protein L20	protein	116	63% helix, 0% strand	Q2FXQ1
U	50S ribosomal protein L21	protein	101	0% helix, 46% strand	Q2FXS8
V	50S ribosomal protein L22	protein	110	19% helix, 35% strand	Q2FW11
W	50S ribosomal protein L23	protein	89	15% helix, 22% strand	Q2FW08
X	50S ribosomal protein L24	protein	96	0% helix, 25% strand	Q2FW17
Y	50S ribosomal protein L25	protein	56	27% helix, 11% strand	Q2G0S0
Z	50S ribosomal protein L27	protein	78	0% helix, 31% strand	Q2FXT0
0	50S ribosomal protein L28	protein	44	0% helix, 9% strand	Q2FZ60
1	50S ribosomal protein L29	protein	65	57% helix, 0% strand	Q2FW14
2	50S ribosomal protein L30	protein	57	14% helix, 23% strand	P0A0G2
4	50S ribosomal protein L32	protein	34	0% helix, 6% strand	Q2FZF1
6	50S ribosomal protein L34	protein	44	39% helix, 0% strand	Q2FUQ0
7	50S ribosomal protein L35	protein	62	0% helix, 11% strand	Q2FXQ0
9	Ribosomal silencing factor rsfs	protein	112	29% helix, 15% strand	Q2G298

Ligands and binding sites

MG · Magnesium ion · metal · 56 copies · chains A, U, O, E, F, 4
K · Potassium ion · metal · 3 copies · chains A

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	902	0.88	0.91	74	MG
2	1025	0.87	0.89	75	MG
3	975	0.85	0.87	92	empty
4	932	0.84	0.87	65	MG
5	888	0.84	0.87	73	MG

Interfaces

49 interfaces between chains.

A–D · 5024 Å² buried · 80 hydrogen bonds · protein-nucleic
A–E · 4998 Å² buried · 79 hydrogen bonds · protein-nucleic
A–O · 4376 Å² buried · 59 hydrogen bonds · protein-nucleic
A–F · 4143 Å² buried · 68 hydrogen bonds · protein-nucleic
A–T · 3976 Å² buried · 43 hydrogen bonds · protein-nucleic

Compared structures

6SJ6 · Cryo-EM structure of 50S-RsfS complex from Staphylococcus aureus · the same entry in another collection · chain Q against Q, 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 P60430
Every structure of UniProt Q2FW06
Every structure of UniProt Q2FW07
Every structure of UniProt Q2FW38
Every structure of UniProt Q2FW16
Every structure of UniProt P0A0F8
Every structure of UniProt Q2FW13
Every structure of UniProt Q2FW33
Every structure of UniProt Q2FW22
Every structure of UniProt Q2FZ42
Every structure of UniProt Q2FXQ1
Every structure of UniProt Q2FXS8
Every structure of UniProt Q2FW11
Every structure of UniProt Q2FW08
Every structure of UniProt Q2FW17
Every structure of UniProt Q2G0S0
Every structure of UniProt Q2FXT0
Every structure of UniProt Q2FZ60
Every structure of UniProt Q2FW14
Every structure of UniProt P0A0G2
Every structure of UniProt Q2FZF1
Every structure of UniProt Q2FUQ0
Every structure of UniProt Q2FXQ0
Every structure of UniProt Q2G298
Elsewhere: RCSB PDB 6SJ6 · PDBe 6SJ6 · UniProt P60430 · UniProt Q2FW06 · UniProt Q2FW07 · UniProt Q2FW38 · UniProt Q2FW16 · UniProt P0A0F8 · UniProt Q2FW13 · UniProt Q2FW33 · UniProt Q2FW22 · UniProt Q2FZ42 · UniProt Q2FXQ1 · UniProt Q2FXS8 · UniProt Q2FW11 · UniProt Q2FW08 · UniProt Q2FW17 · UniProt Q2G0S0 · UniProt Q2FXT0 · UniProt Q2FZ60 · UniProt Q2FW14 · UniProt P0A0G2 · UniProt Q2FZF1 · UniProt Q2FUQ0 · UniProt Q2FXQ0 · UniProt Q2G298

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