Research workbench

Structure of the E. COLI 50S subunit with ermcl nascent chain

Analyse Structure of the E. COLI 50S subunit with ermcl nascent chain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3J7Z
Type: protein + RNA
Length: 6,428 residues
Chains: 35
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L32; 50S ribosomal protein L33; 50S ribosomal protein L34; 50S…
UniProt: P0A7N4, P0A7N9, P0A7P5, P0A7Q1, P0A7Q6, P0A7J3, P0A7K2, P60422, P60438, P60723, P62399, P0AG55, P0A7R1, P0A7J7, P0AA10, P0ADY3, P02413, P0ADY7, P0AG44, P0C018, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P68919, P0A7L8, P0A7M2, P0A7M6, P0AG51, P03063
Ligands: ERY
Pockets: 20 · best druggability 0.87

Structure

electron microscopy · 35 distinct chains · 24% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	50S ribosomal protein L32	protein	56	18% helix, 18% strand	P0A7N4
1	50S ribosomal protein L33	protein	50	0% helix, 48% strand	P0A7N9
2	50S ribosomal protein L34	protein	46	54% helix, 0% strand	P0A7P5
3	50S ribosomal protein L35	protein	64	27% helix, 3% strand	P0A7Q1
4	50S ribosomal protein L36	protein	38	8% helix, 29% strand	P0A7Q6
5	50S ribosomal protein L10	protein	148	36% helix, 3% strand	P0A7J3
6	50S ribosomal protein L7/L12	protein	30	37% helix, 0% strand	P0A7K2
7	P-tRNA cca-end	rna	3	—	—
A	23S rRNA	rna	2854	—	—
B	5S rRNA	rna	118	—	—
C	50S ribosomal protein L2	protein	271	8% helix, 20% strand	P60422
D	50S ribosomal protein L3	protein	209	7% helix, 25% strand	P60438
E	50S ribosomal protein L4	protein	201	31% helix, 4% strand	P60723
F	50S ribosomal protein L5	protein	177	36% helix, 16% strand	P62399
G	50S ribosomal protein L6	protein	176	18% helix, 23% strand	P0AG55
H	50S ribosomal protein L9	protein	50	28% helix, 10% strand	P0A7R1
I	50S ribosomal protein L11	protein	141	18% helix, 4% strand	P0A7J7
J	50S ribosomal protein L13	protein	142	32% helix, 14% strand	P0AA10
K	50S ribosomal protein L14	protein	122	9% helix, 35% strand	P0ADY3
L	50S ribosomal protein L15	protein	143	15% helix, 10% strand	P02413
M	50S ribosomal protein L16	protein	136	20% helix, 21% strand	P0ADY7
N	50S ribosomal protein L17	protein	120	48% helix, 13% strand	P0AG44
O	50S ribosomal protein L18	protein	116	41% helix, 16% strand	P0C018
P	50S ribosomal protein L19	protein	114	18% helix, 32% strand	P0A7K6
Q	50S ribosomal protein L20	protein	117	76% helix, 0% strand	P0A7L3
R	50S ribosomal protein L21	protein	103	0% helix, 54% strand	P0AG48
S	50S ribosomal protein L22	protein	110	32% helix, 32% strand	P61175
T	50S ribosomal protein L23	protein	93	19% helix, 18% strand	P0ADZ0
U	50S ribosomal protein L24	protein	102	3% helix, 39% strand	P60624
V	50S ribosomal protein L25	protein	94	22% helix, 43% strand	P68919
W	50S ribosomal protein L27	protein	79	0% helix, 10% strand	P0A7L8
X	50S ribosomal protein L28	protein	77	22% helix, 21% strand	P0A7M2
Y	50S ribosomal protein L29	protein	63	67% helix, 0% strand	P0A7M6
Z	50S ribosomal protein L30	protein	58	38% helix, 17% strand	P0AG51
a	Ermcl nascent chain	protein	7	0% helix, 0% strand	P03063

Ligands and binding sites

ERY · Erythromycin A · ligand · chains A, S, a

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	1122	0.87	0.89	98	empty
2	569	0.85	0.92	67	empty
3	584	0.85	0.91	77	empty
4	923	0.85	0.87	73	empty
5	884	0.84	0.87	69	empty

Interfaces

64 interfaces between chains.

A–C · 7190 Å² buried · 213 hydrogen bonds · protein-nucleic
A–D · 5023 Å² buried · 113 hydrogen bonds · protein-nucleic
A–L · 4477 Å² buried · 126 hydrogen bonds · protein-nucleic
A–E · 4216 Å² buried · 95 hydrogen bonds · protein-nucleic
A–Q · 4139 Å² buried · 110 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 3 disulfide (disulfide).

Compared structures

3J7Z · Structure of the E. coli 50S subunit with ErmCL nascent chain · the same entry in another collection · chain C against C, 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 P0A7N4
Every structure of UniProt P0A7N9
Every structure of UniProt P0A7P5
Every structure of UniProt P0A7Q1
Every structure of UniProt P0A7Q6
Every structure of UniProt P0A7J3
Every structure of UniProt P0A7K2
Every structure of UniProt P60422
Every structure of UniProt P60438
Every structure of UniProt P60723
Every structure of UniProt P62399
Every structure of UniProt P0AG55
Every structure of UniProt P0A7R1
Every structure of UniProt P0A7J7
Every structure of UniProt P0AA10
Every structure of UniProt P0ADY3
Every structure of UniProt P02413
Every structure of UniProt P0ADY7
Every structure of UniProt P0AG44
Every structure of UniProt P0C018
Every structure of UniProt P0A7K6
Every structure of UniProt P0A7L3
Every structure of UniProt P0AG48
Every structure of UniProt P61175
Every structure of UniProt P0ADZ0
Every structure of UniProt P60624
Every structure of UniProt P68919
Every structure of UniProt P0A7L8
Every structure of UniProt P0A7M2
Every structure of UniProt P0A7M6
Every structure of UniProt P0AG51
Every structure of UniProt P03063
Elsewhere: RCSB PDB 3J7Z · PDBe 3J7Z · UniProt P0A7N4 · UniProt P0A7N9 · UniProt P0A7P5 · UniProt P0A7Q1 · UniProt P0A7Q6 · UniProt P0A7J3 · UniProt P0A7K2 · UniProt P60422 · UniProt P60438 · UniProt P60723 · UniProt P62399 · UniProt P0AG55 · UniProt P0A7R1 · UniProt P0A7J7 · UniProt P0AA10 · UniProt P0ADY3 · UniProt P02413 · UniProt P0ADY7 · UniProt P0AG44 · UniProt P0C018 · UniProt P0A7K6 · UniProt P0A7L3 · UniProt P0AG48 · UniProt P61175 · UniProt P0ADZ0 · UniProt P60624 · UniProt P68919 · UniProt P0A7L8 · UniProt P0A7M2 · UniProt P0A7M6 · UniProt P0AG51 · UniProt P03063

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