MolNFT v2 · #228350 · protein + RNA

70S Escherichia coli ribosome with P-site initiatior tRNA.

9FBV · Large ribosomal subunit protein bL33: “70S Escherichia coli ribosome with P-site initiatior tRNA.”. Electron microscopy at 2.4, 3 ligands (MG, K, ZN), 20 pockets (best druggability 0.87). MolNFT v2 #228350 on GenesisL1: 3D…

PDB: 9FBV
Type: protein + RNA
Length: 10,054 residues
Chains: 54
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.4
Source: Escherichia coli BW25113
Molecule: Large ribosomal subunit protein bL33; Large ribosomal subunit protein bL34; Large…
UniProt: P0A7N9, P0A7P5, P0A7Q1, P0A7Q6, P60422, P60438, P60723, P62399, P0AG55, P0A7R1, P0AA10, P02413, P0ADY7, P0AG44, P0C018, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P68919, P0A7L8, P0A7M2, P0A7M6, P0AG51, P0A7N4, P0A7M9, P0ADY3, P0A7V0, P0A7V8, P0A7W1, P02358, P0A7W7, P0A7R9, P0A7S3, P0ADZ4, P0A7T3, P0AG63, P0A7T7, P0A7U7, P68679, P0A7V3, P02359, P0A7X3, P0A7R5, P0A7S9, P0AG59, P0A7U3
Ligands: MG, K, ZN
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · resolution 2.4 · 54 distinct chains · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	Large ribosomal subunit protein bL33	protein	51	0% helix, 55% strand	P0A7N9
1	Large ribosomal subunit protein bL34	protein	46	59% helix, 0% strand	P0A7P5
2	Large ribosomal subunit protein bL35	protein	64	33% helix, 11% strand	P0A7Q1
3	Large ribosomal subunit protein bL36A	protein	38	8% helix, 42% strand	P0A7Q6
b	5S ribosomal RNA	rna	119	—	—
c	Large ribosomal subunit protein uL2	protein	271	8% helix, 29% strand	P60422
d	Large ribosomal subunit protein uL3	protein	209	10% helix, 37% strand	P60438
e	Large ribosomal subunit protein uL4	protein	201	35% helix, 12% strand	P60723
f	Large ribosomal subunit protein uL5	protein	177	39% helix, 20% strand	P62399
g	Large ribosomal subunit protein uL6	protein	176	22% helix, 35% strand	P0AG55
h	Large ribosomal subunit protein bL9	protein	41	27% helix, 29% strand	P0A7R1
i	Large ribosomal subunit protein uL13	protein	142	34% helix, 19% strand	P0AA10
k	50S ribosomal protein L15	protein	144	22% helix, 14% strand	P02413
l	Large ribosomal subunit protein uL16	protein	136	20% helix, 28% strand	P0ADY7
m	Large ribosomal subunit protein bL17	protein	118	49% helix, 17% strand	P0AG44
n	Large ribosomal subunit protein uL18	protein	116	46% helix, 20% strand	P0C018
o	Large ribosomal subunit protein bL19	protein	114	18% helix, 45% strand	P0A7K6
p	Large ribosomal subunit protein bL20	protein	117	79% helix, 0% strand	P0A7L3
q	Large ribosomal subunit protein bL21	protein	103	0% helix, 64% strand	P0AG48
r	Large ribosomal subunit protein uL22	protein	110	42% helix, 35% strand	P61175
s	Large ribosomal subunit protein uL23	protein	93	30% helix, 38% strand	P0ADZ0
t	Large ribosomal subunit protein uL24	protein	102	3% helix, 45% strand	P60624
u	50S ribosomal protein L25	protein	94	21% helix, 45% strand	P68919
v	Large ribosomal subunit protein bL27	protein	83	0% helix, 39% strand	P0A7L8
w	Large ribosomal subunit protein bL28	protein	77	26% helix, 36% strand	P0A7M2
x	Large ribosomal subunit protein uL29	protein	62	82% helix, 0% strand	P0A7M6
y	Large ribosomal subunit protein uL30	protein	58	33% helix, 26% strand	P0AG51
z	Large ribosomal subunit protein bL32	protein	56	18% helix, 16% strand	P0A7N4
4	Large ribosomal subunit protein bL31A	protein	60	22% helix, 20% strand	P0A7M9
a	23S ribosomal RNA	rna	2753	—	—
j	Large ribosomal subunit protein uL14	protein	118	5% helix, 41% strand	P0ADY3
B	30S ribosomal protein S2	protein	224	53% helix, 13% strand	P0A7V0
D	Small ribosomal subunit protein uS4	protein	205	45% helix, 10% strand	P0A7V8
E	Small ribosomal subunit protein uS5	protein	156	32% helix, 38% strand	P0A7W1
F	30S ribosomal protein S6, fully modified isoform	protein	103	29% helix, 47% strand	P02358
H	Small ribosomal subunit protein uS8	protein	129	27% helix, 35% strand	P0A7W7
K	Small ribosomal subunit protein uS11	protein	117	21% helix, 29% strand	P0A7R9
L	Small ribosomal subunit protein uS12	protein	123	7% helix, 28% strand	P0A7S3
O	Small ribosomal subunit protein uS15	protein	88	76% helix, 0% strand	P0ADZ4
P	30S ribosomal protein S16	protein	81	25% helix, 36% strand	P0A7T3
Q	Small ribosomal subunit protein uS17	protein	79	0% helix, 62% strand	P0AG63
R	Small ribosomal subunit protein bS18	protein	66	47% helix, 3% strand	P0A7T7
T	30S ribosomal protein S20	protein	86	88% helix, 0% strand	P0A7U7
U	Small ribosomal subunit protein bS21	protein	70	67% helix, 4% strand	P68679
X	messenger RNA	rna	3	—	—
C	Small ribosomal subunit protein uS3	protein	206	37% helix, 31% strand	P0A7V3
G	30S ribosomal protein S7	protein	153	59% helix, 9% strand	P02359
I	Small ribosomal subunit protein uS9	protein	127	35% helix, 20% strand	P0A7X3
J	Small ribosomal subunit protein uS10	protein	98	28% helix, 45% strand	P0A7R5
M	Small ribosomal subunit protein uS13	protein	115	50% helix, 5% strand	P0A7S9
N	Small ribosomal subunit protein uS14	protein	100	57% helix, 7% strand	P0AG59
S	Small ribosomal subunit protein uS19	protein	84	27% helix, 18% strand	P0A7U3
A	16S ribosomal RNA	rna	1519	—	—
Z	fMet-tRNA	rna	73	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 306 copies · chains b, u, c, a, d, k, z, e, 2, s, i, m, p, l, v, A, N, M, X, Q, o, E
K · Potassium ion · metal · 3 copies · chains d, a, X, A
ZN · Zinc ion · metal · 2 copies · chains 3, 4

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	1098	0.87	0.89	93	MG
2	872	0.87	0.90	85	MG
3	1117	0.85	0.87	94	MG
4	1024	0.85	0.86	100	MG
5	698	0.85	0.89	64	MG

Interfaces

121 interfaces between chains.

c–a · 7167 Å² buried · 207 hydrogen bonds · protein-nucleic
d–a · 5081 Å² buried · 133 hydrogen bonds · protein-nucleic
k–a · 4487 Å² buried · 130 hydrogen bonds · protein-nucleic
e–a · 4218 Å² buried · 109 hydrogen bonds · protein-nucleic
p–a · 4111 Å² buried · 124 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 38 modified, 1 disulfide (nucleotide modification, nonstandard, disulfide).

Compared structures

P0A7M9 · AlphaFold monomer V2.0 prediction for 50S ribosomal protein L31 (P0A7M9) · a predicted model of the same protein · chain 4 against A, TM-score 0.83

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