Research workbench

30S subunit (head) of 70S ribosome enterococcus faecalis multibody refinement

Analyse 30S subunit (head) of 70S ribosome enterococcus faecalis multibody refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WUA
Type: protein + RNA
Length: 1,235 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16S rRNA; 30S ribosomal protein S3; 30S ribosomal protein S7; 30S ribosomal protein S9…
UniProt: A0A1B4XKR8, A0A1B4XKQ3, A0A1B4XSA2, A0A1B4XKR5, A0A1B4XKT7, A0A1B4XKT0, A0A1B4XKS0
Ligands: ZN
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 8 distinct chains · 34% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	16S rRNA	rna	402	—	—
c	30S ribosomal protein S3	protein	204	30% helix, 27% strand	A0A1B4XKR8
g	30S ribosomal protein S7	protein	154	53% helix, 8% strand	A0A1B4XKQ3
i	30S ribosomal protein S9	protein	128	29% helix, 24% strand	A0A1B4XSA2
j	30S ribosomal protein S10	protein	99	22% helix, 38% strand	A0A1B4XKR5
m	30S ribosomal protein S13	protein	110	46% helix, 0% strand	A0A1B4XKT7
n	30S ribosomal protein S14 type Z	protein	60	30% helix, 10% strand	A0A1B4XKT0
s	30S ribosomal protein S19	protein	78	18% helix, 18% strand	A0A1B4XKS0

Ligands and binding sites

ZN · Zinc ion · metal · chains n

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	910	0.85	0.88	54	empty
2	956	0.85	0.86	79	empty
3	814	0.82	0.86	70	empty
4	836	0.81	0.84	67	empty
5	885	0.79	0.82	73	empty

Interfaces

14 interfaces between chains.

a–i · 2868 Å² buried · 45 hydrogen bonds · protein-nucleic
a–n · 1835 Å² buried · 33 hydrogen bonds · protein-nucleic
a–j · 1736 Å² buried · 18 hydrogen bonds · protein-nucleic
a–m · 1715 Å² buried · 41 hydrogen bonds · protein-nucleic
a–g · 1463 Å² buried · 27 hydrogen bonds · protein-nucleic

Compared structures

6WUA · 30S subunit (head) of 70S Ribosome Enterococcus faecalis MultiBody refinement · the same entry in another collection · chain a against a, 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 A0A1B4XKR8
Every structure of UniProt A0A1B4XKQ3
Every structure of UniProt A0A1B4XSA2
Every structure of UniProt A0A1B4XKR5
Every structure of UniProt A0A1B4XKT7
Every structure of UniProt A0A1B4XKT0
Every structure of UniProt A0A1B4XKS0
Elsewhere: RCSB PDB 6WUA · PDBe 6WUA · UniProt A0A1B4XKR8 · UniProt A0A1B4XKQ3 · UniProt A0A1B4XSA2 · UniProt A0A1B4XKR5 · UniProt A0A1B4XKT7 · UniProt A0A1B4XKT0 · UniProt A0A1B4XKS0

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