MolNFT v1 · #164171 · protein + RNA

Pseudomonas aeruginosa 30S ribosome from a clinical isolate

6SPE · 16S ribosomal RNA: “Pseudomonas aeruginosa 30S ribosome from a clinical isolate”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #164171 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6SPE
Type: protein + RNA
Length: 3,918 residues
Chains: 21
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16S ribosomal RNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal…
UniProt: A0A072ZPV8, A0A140S919, A0A072ZDF7, A0A241XG65, A0A069Q263, A0A2V3F2U6, E2RXT9, A0A069PXX1, E2RXT0, E2RXU4, A0A071L394, E2RXU3, E2RXT8, A0A071L3R7, A0A2V4FRZ2, E2RXT5, A0A2V3DLV3, E2RXT2, A0A072ZDZ9, A0A069QC99
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 21 distinct chains · 32% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
a	16S ribosomal RNA	rna	1526	—	—
b	30S ribosomal protein S2	protein	234	40% helix, 8% strand	A0A072ZPV8
c	30S ribosomal protein S3	protein	205	27% helix, 22% strand	A0A140S919
d	30S ribosomal protein S4	protein	205	37% helix, 4% strand	A0A072ZDF7
e	30S ribosomal protein S5	protein	156	18% helix, 31% strand	A0A241XG65
f	30S ribosomal protein S6	protein	105	30% helix, 26% strand	A0A069Q263
g	30S ribosomal protein S7	protein	154	46% helix, 3% strand	A0A2V3F2U6
h	30S ribosomal protein S8	protein	129	22% helix, 28% strand	E2RXT9
i	30S ribosomal protein S9	protein	126	26% helix, 22% strand	A0A069PXX1
j	30S ribosomal protein S10	protein	96	20% helix, 32% strand	E2RXT0
k	30S ribosomal protein S11	protein	115	10% helix, 30% strand	E2RXU4
l	30S ribosomal protein S12	protein	121	3% helix, 28% strand	A0A071L394
m	30S ribosomal protein S13	protein	110	45% helix, 2% strand	E2RXU3
n	30S ribosomal protein S14	protein	98	44% helix, 3% strand	E2RXT8
o	30S ribosomal protein S15	protein	86	67% helix, 0% strand	A0A071L3R7
p	30S ribosomal protein S16	protein	78	15% helix, 24% strand	A0A2V4FRZ2
q	30S ribosomal protein S17	protein	76	0% helix, 50% strand	E2RXT5
r	30S ribosomal protein S18	protein	71	44% helix, 3% strand	A0A2V3DLV3
s	30S ribosomal protein S19	protein	80	19% helix, 19% strand	E2RXT2
t	30S ribosomal protein S20	protein	85	73% helix, 0% strand	A0A072ZDZ9
u	30S ribosomal protein S21	protein	62	69% helix, 2% strand	A0A069QC99

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	814	0.85	0.88	81	empty
2	712	0.84	0.88	64	empty
3	746	0.84	0.88	61	empty
4	1011	0.84	0.86	63	empty
5	527	0.82	0.89	55	empty

Interfaces

39 interfaces between chains.

a–d · 2975 Å² buried · 48 hydrogen bonds · protein-nucleic
a–l · 2940 Å² buried · 48 hydrogen bonds · protein-nucleic
a–i · 2671 Å² buried · 49 hydrogen bonds · protein-nucleic
a–t · 2235 Å² buried · 30 hydrogen bonds · protein-nucleic
a–p · 2112 Å² buried · 22 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6SPE · Pseudomonas aeruginosa 30s ribosome from a clinical isolate · the same entry in another collection · chain l against l, 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 A0A072ZPV8
Every structure of UniProt A0A140S919
Every structure of UniProt A0A072ZDF7
Every structure of UniProt A0A241XG65
Every structure of UniProt A0A069Q263
Every structure of UniProt A0A2V3F2U6
Every structure of UniProt E2RXT9
Every structure of UniProt A0A069PXX1
Every structure of UniProt E2RXT0
Every structure of UniProt E2RXU4
Every structure of UniProt A0A071L394
Every structure of UniProt E2RXU3
Every structure of UniProt E2RXT8
Every structure of UniProt A0A071L3R7
Every structure of UniProt A0A2V4FRZ2
Every structure of UniProt E2RXT5
Every structure of UniProt A0A2V3DLV3
Every structure of UniProt E2RXT2
Every structure of UniProt A0A072ZDZ9
Every structure of UniProt A0A069QC99
Elsewhere: RCSB PDB 6SPE · PDBe 6SPE · UniProt A0A072ZPV8 · UniProt A0A140S919 · UniProt A0A072ZDF7 · UniProt A0A241XG65 · UniProt A0A069Q263 · UniProt A0A2V3F2U6 · UniProt E2RXT9 · UniProt A0A069PXX1 · UniProt E2RXT0 · UniProt E2RXU4 · UniProt A0A071L394 · UniProt E2RXU3 · UniProt E2RXT8 · UniProt A0A071L3R7 · UniProt A0A2V4FRZ2 · UniProt E2RXT5 · UniProt A0A2V3DLV3 · UniProt E2RXT2 · UniProt A0A072ZDZ9 · UniProt A0A069QC99

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