MolNFT v1 · #171097 · protein + RNA

Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit body

6YT9 · 16S ribosomal RNA: “Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit body”. Electron microscopy, 1 ligand (MG), 20 pockets (best druggability 0.85). MolNFT v1 #171097 on GenesisL1: 3D structure, binding sites and…

PDB: 6YT9
Type: protein + RNA
Length: 2,536 residues
Chains: 15
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16S ribosomal RNA; 30S ribosomal protein S2; 30S ribosomal protein S4; 30S ribosomal…
UniProt: D0CC74, D0CD21, D0CD14, D0C5Z0, D0CD11, D0CD20, D0C9P6, D0CAU9, D0CCR5, D0CD06, D0C5Y9, D0C7N1, D0C5Q3
Ligands: MG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 15 distinct chains · 35% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	16S ribosomal RNA	rna	894	—	—
4	16S ribosomal RNA	rna	146	—	—
c	30S ribosomal protein S2	protein	219	40% helix, 12% strand	D0CC74
e	30S ribosomal protein S4	protein	207	36% helix, 6% strand	D0CD21
f	30S ribosomal protein S5	protein	155	27% helix, 39% strand	D0CD14
g	30S ribosomal protein S6	protein	103	28% helix, 40% strand	D0C5Z0
i	30S ribosomal protein S8	protein	130	24% helix, 35% strand	D0CD11
l	30S ribosomal protein S11	protein	114	22% helix, 29% strand	D0CD20
m	30S ribosomal protein S12	protein	122	10% helix, 29% strand	D0C9P6
p	30S ribosomal protein S15	protein	88	75% helix, 0% strand	D0CAU9
q	30S ribosomal protein S16	protein	80	23% helix, 33% strand	D0CCR5
r	30S ribosomal protein S17	protein	79	0% helix, 65% strand	D0CD06
s	30S ribosomal protein S18	protein	53	51% helix, 4% strand	D0C5Y9
u	30S ribosomal protein S20	protein	86	85% helix, 0% strand	D0C7N1
v	30S ribosomal protein S21	protein	60	62% helix, 3% strand	D0C5Q3

Ligands and binding sites

MG · Magnesium ion · metal · 56 copies · chains 2, l, u, 4, v

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	1074	0.85	0.86	109	MG
2	728	0.83	0.88	58	MG
3	791	0.81	0.85	56	MG
4	551	0.81	0.88	57	MG
5	584	0.80	0.87	54	MG

Interfaces

28 interfaces between chains.

2–4 · 3071 Å² buried · 102 hydrogen bonds · nucleic-nucleic
2–e · 3050 Å² buried · 85 hydrogen bonds · protein-nucleic
2–m · 2766 Å² buried · 66 hydrogen bonds · protein-nucleic
2–q · 2201 Å² buried · 45 hydrogen bonds · protein-nucleic
2–u · 2079 Å² buried · 50 hydrogen bonds · protein-nucleic

Compared structures

6YT9 · Acinetobacter baumannii ribosome-tigecycline complex - 30S subunit body · the same entry in another collection · chain 2 against 2, 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 D0CC74
Every structure of UniProt D0CD21
Every structure of UniProt D0CD14
Every structure of UniProt D0C5Z0
Every structure of UniProt D0CD11
Every structure of UniProt D0CD20
Every structure of UniProt D0C9P6
Every structure of UniProt D0CAU9
Every structure of UniProt D0CCR5
Every structure of UniProt D0CD06
Every structure of UniProt D0C5Y9
Every structure of UniProt D0C7N1
Every structure of UniProt D0C5Q3
Elsewhere: RCSB PDB 6YT9 · PDBe 6YT9 · UniProt D0CC74 · UniProt D0CD21 · UniProt D0CD14 · UniProt D0C5Z0 · UniProt D0CD11 · UniProt D0CD20 · UniProt D0C9P6 · UniProt D0CAU9 · UniProt D0CCR5 · UniProt D0CD06 · UniProt D0C5Y9 · UniProt D0C7N1 · UniProt D0C5Q3

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