MolNFT v1 · #14803 · protein + RNA

Structure of the E. COLI ribosomal termination complex with release factor 2

1ML5 · T-RNA(PHE): “Structure of the E. COLI ribosomal termination complex with release factor 2”. Electron microscopy, 14 pockets (best druggability 0.67). MolNFT v1 #14803 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1ML5
Type: protein + RNA
Length: 5,171 residues
Chains: 42
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: T-RNA(PHE); A- and P-site messenger RNA codons; Peptide chain release factor 2; 30S…
UniProt: P07012
Pockets: 14 · best druggability 0.67

Structure

electron microscopy · 42 distinct chains · 0% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	T-RNA(PHE)	rna	76	—	—
C	A- and P-site messenger RNA codons	rna	6	—	—
Z	Peptide chain release factor 2	protein	362	0% helix, 0% strand	P07012
E	30S ribosomal protein S2	protein	234	0% helix, 0% strand	—
F	30S ribosomal protein S3	protein	206	0% helix, 0% strand	—
G	30S ribosomal protein S4	protein	208	0% helix, 0% strand	—
H	30S ribosomal protein S5	protein	150	0% helix, 0% strand	—
I	30S ribosomal protein S6	protein	101	0% helix, 0% strand	—
J	30S ribosomal protein S7	protein	155	0% helix, 0% strand	—
K	30S ribosomal protein S8	protein	138	0% helix, 0% strand	—
L	30S ribosomal protein S9	protein	127	0% helix, 0% strand	—
M	30S ribosomal protein S10	protein	98	0% helix, 0% strand	—
N	30S ribosomal protein S11	protein	119	0% helix, 0% strand	—
O	30S ribosomal protein S12	protein	124	0% helix, 0% strand	—
P	30S ribosomal protein S13	protein	125	0% helix, 0% strand	—
Q	30S ribosomal protein S14	protein	60	0% helix, 0% strand	—
R	30S ribosomal protein S15	protein	88	0% helix, 0% strand	—
S	30S ribosomal protein S16	protein	83	0% helix, 0% strand	—
T	30S ribosomal protein S17	protein	104	0% helix, 0% strand	—
U	30S ribosomal protein S18	protein	73	0% helix, 0% strand	—
V	30S ribosomal protein S19	protein	80	0% helix, 0% strand	—
W	30S ribosomal protein S20	protein	99	0% helix, 0% strand	—
X	30S ribosomal protein thx	protein	24	0% helix, 0% strand	—
c	50S ribosomal protein L1	protein	224	0% helix, 0% strand	—
d	50S ribosomal protein L2	protein	173	0% helix, 0% strand	—
e	50S ribosomal protein L3	protein	191	0% helix, 0% strand	—
f	50S ribosomal protein L4	protein	189	0% helix, 0% strand	—
g	50S ribosomal protein L5	protein	122	0% helix, 0% strand	—
h	50S ribosomal protein L6	protein	164	0% helix, 0% strand	—
l	50S ribosomal protein L11	protein	133	0% helix, 0% strand	—
m	50S ribosomal protein L13	protein	117	0% helix, 0% strand	—
n	50S ribosomal protein L14	protein	122	0% helix, 0% strand	—
o	50S ribosomal protein L15	protein	84	0% helix, 0% strand	—
p	50S ribosomal protein L16	protein	138	0% helix, 0% strand	—
q	50S ribosomal protein L18	protein	113	0% helix, 0% strand	—
r	50S ribosomal protein L19	protein	52	0% helix, 0% strand	—
s	50S ribosomal protein L22	protein	110	0% helix, 0% strand	—
t	50S ribosomal protein L23	protein	76	0% helix, 0% strand	—
u	50S ribosomal protein L24	protein	110	0% helix, 0% strand	—
v	50S ribosomal protein L25	protein	89	0% helix, 0% strand	—
w	50S ribosomal protein L29	protein	64	0% helix, 0% strand	—
x	50S ribosomal protein L30	protein	60	0% helix, 0% strand	—

Pockets

14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	880	0.67	0.74	49	empty
2	330	0.54	0.76	28	empty
3	222	0.50	0.74	58	empty
4	169	0.46	0.73	45	empty
5	105	0.38	0.73	29	empty

Interfaces

22 interfaces between chains.

B–Z · 337 Å² buried · 0 hydrogen bonds · protein-nucleic
I–U · 175 Å² buried · 0 hydrogen bonds · protein-protein
M–Q · 159 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 156 Å² buried · 8 hydrogen bonds · nucleic-nucleic
n–r · 118 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 modified (nucleotide modification).

Compared structures

1ML5 · Structure of the E. coli ribosomal termination complex with release factor 2 · 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 P07012
Elsewhere: RCSB PDB 1ML5 · PDBe 1ML5 · UniProt P07012

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