MolNFT v1 · #184117 · protein + RNA

E. COLI pre-30S delta rbfa ribosomal subunit class F

7OE0 · 30S ribosomal protein S2: “E. COLI pre-30S delta rbfa ribosomal subunit class F”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #184117 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7OE0
Type: protein + RNA
Length: 3,718 residues
Chains: 20
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 30S ribosomal protein S2; 30S ribosomal protein S4; 30S ribosomal protein S5; 30S…
UniProt: A0A6D2W584, A0A6D2XM56, A0A6D2YBZ5, P02358, A0A6D2XYQ3, A0A6D2X4T2, A0A4S5B3M5, C3SSQ8, A0A6D2XXS6, A0A4S5APA8, A0A6D2XHZ3, A0A4S5B3X7, A0A6D2XYP0, P02359, A0A6D2XBM7, A0A6D2XQX6, A0A6D2XQ78, A0A6D2WD65, A0A6D2WKS9
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 20 distinct chains · 35% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	30S ribosomal protein S2	protein	218	44% helix, 11% strand	A0A6D2W584
D	30S ribosomal protein S4	protein	205	41% helix, 8% strand	A0A6D2XM56
E	30S ribosomal protein S5	protein	150	27% helix, 35% strand	A0A6D2YBZ5
F	30S ribosomal protein S6, fully modified isoform	protein	100	30% helix, 29% strand	P02358
H	30S ribosomal protein S8	protein	129	27% helix, 30% strand	A0A6D2XYQ3
K	30S ribosomal protein S11	protein	95	23% helix, 14% strand	A0A6D2X4T2
L	30S ribosomal protein S12	protein	123	10% helix, 26% strand	A0A4S5B3M5
O	30S ribosomal protein S15	protein	88	74% helix, 0% strand	C3SSQ8
P	30S ribosomal protein S16	protein	82	26% helix, 37% strand	A0A6D2XXS6
Q	30S ribosomal protein S17	protein	80	0% helix, 60% strand	A0A4S5APA8
R	30S ribosomal protein S18	protein	50	46% helix, 0% strand	A0A6D2XHZ3
T	30S ribosomal protein S20	protein	85	85% helix, 0% strand	A0A4S5B3X7
A	16S rRNA	rna	1510	—	—
C	30S ribosomal protein S3	protein	206	34% helix, 22% strand	A0A6D2XYP0
G	30S ribosomal protein S7	protein	83	48% helix, 2% strand	P02359
I	30S ribosomal protein S9	protein	127	33% helix, 15% strand	A0A6D2XBM7
J	30S ribosomal protein S10	protein	98	18% helix, 28% strand	A0A6D2XQX6
M	30S ribosomal protein S13	protein	114	37% helix, 0% strand	A0A6D2XQ78
N	30S ribosomal protein S14	protein	96	47% helix, 4% strand	A0A6D2WD65
S	30S ribosomal protein S19	protein	79	16% helix, 16% strand	A0A6D2WKS9

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	1111	0.87	0.89	84	empty
2	644	0.85	0.90	73	empty
3	799	0.85	0.88	95	empty
4	857	0.83	0.86	70	empty
5	1066	0.83	0.85	81	empty

Interfaces

33 interfaces between chains.

D–A · 3064 Å² buried · 80 hydrogen bonds · protein-nucleic
A–I · 3022 Å² buried · 97 hydrogen bonds · protein-nucleic
L–A · 2882 Å² buried · 74 hydrogen bonds · protein-nucleic
A–N · 2384 Å² buried · 75 hydrogen bonds · protein-nucleic
T–A · 2368 Å² buried · 59 hydrogen bonds · protein-nucleic

Compared structures

7OE0 · E. coli pre-30S delta rbfA ribosomal subunit class F · the same entry in another collection · chain B against B, 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 A0A6D2W584
Every structure of UniProt A0A6D2XM56
Every structure of UniProt A0A6D2YBZ5
Every structure of UniProt P02358
Every structure of UniProt A0A6D2XYQ3
Every structure of UniProt A0A6D2X4T2
Every structure of UniProt A0A4S5B3M5
Every structure of UniProt C3SSQ8
Every structure of UniProt A0A6D2XXS6
Every structure of UniProt A0A4S5APA8
Every structure of UniProt A0A6D2XHZ3
Every structure of UniProt A0A4S5B3X7
Every structure of UniProt A0A6D2XYP0
Every structure of UniProt P02359
Every structure of UniProt A0A6D2XBM7
Every structure of UniProt A0A6D2XQX6
Every structure of UniProt A0A6D2XQ78
Every structure of UniProt A0A6D2WD65
Every structure of UniProt A0A6D2WKS9
Elsewhere: RCSB PDB 7OE0 · PDBe 7OE0 · UniProt A0A6D2W584 · UniProt A0A6D2XM56 · UniProt A0A6D2YBZ5 · UniProt P02358 · UniProt A0A6D2XYQ3 · UniProt A0A6D2X4T2 · UniProt A0A4S5B3M5 · UniProt C3SSQ8 · UniProt A0A6D2XXS6 · UniProt A0A4S5APA8 · UniProt A0A6D2XHZ3 · UniProt A0A4S5B3X7 · UniProt A0A6D2XYP0 · UniProt P02359 · UniProt A0A6D2XBM7 · UniProt A0A6D2XQX6 · UniProt A0A6D2XQ78 · UniProt A0A6D2WD65 · UniProt A0A6D2WKS9

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