Research workbench

Electron cryo-microscopy structure of enga bound with the 50S ribosomal subunit

Analyse Electron cryo-microscopy structure of enga bound with the 50S ribosomal subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3J8G
Type: protein + RNA
Length: 6,954 residues
Chains: 32
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5S rRNA; 23S rRNA; 50S ribosomal protein L28; 50S ribosomal protein L14; 50S ribosomal…
UniProt: C9QUM4, C9QXH2, P02413, C9QXH0, C9QXG9, C9QXI8, C9QXH8, C9R119, C9QTZ1, C9QY61, C9QXG7, C9QXG2, B1X6G9, C9QXI0, C9QXH3, C9QRC1, C9QPR2, C9QXG3, C9QY62, C9QYM3, H0QFK1, C9QXD2, C9QTZ0, C9QXI3, C9QXG5, C9QXH4, C9QXH7, C9QTM2, C9QV94, C9QXP2
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 32 distinct chains · 21% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5S rRNA	rna	115	—	—
B	23S rRNA	rna	2874	—	—
0	50S ribosomal protein L28	protein	77	16% helix, 10% strand	C9QUM4
K	50S ribosomal protein L14	protein	121	7% helix, 28% strand	C9QXH2
L	50S ribosomal protein L15	protein	143	10% helix, 7% strand	P02413
1	50S ribosomal protein L29	protein	63	68% helix, 0% strand	C9QXH0
M	50S ribosomal protein L16	protein	136	18% helix, 25% strand	C9QXG9
N	50S ribosomal protein L17	protein	120	46% helix, 14% strand	C9QXI8
O	50S ribosomal protein L18	protein	116	27% helix, 19% strand	C9QXH8
P	50S ribosomal protein L19	protein	114	10% helix, 18% strand	C9R119
Q	50S ribosomal protein L20	protein	117	67% helix, 0% strand	C9QTZ1
R	50S ribosomal protein L21	protein	103	0% helix, 40% strand	C9QY61
S	50S ribosomal protein L22	protein	110	25% helix, 42% strand	C9QXG7
D	50S ribosomal protein L3	protein	209	6% helix, 25% strand	C9QXG2
T	50S ribosomal protein L23	protein	93	14% helix, 19% strand	B1X6G9
2	50S ribosomal protein L30	protein	58	22% helix, 21% strand	C9QXI0
U	50S ribosomal protein L24	protein	99	3% helix, 31% strand	C9QXH3
W	50S ribosomal protein L25	protein	94	20% helix, 50% strand	C9QRC1
X	GTPase der	protein	418	32% helix, 18% strand	C9QPR2
E	50S ribosomal protein L4	protein	201	32% helix, 5% strand	C9QXG3
Y	50S ribosomal protein L27	protein	79	0% helix, 5% strand	C9QY62
3	50S ribosomal protein L32	protein	56	13% helix, 7% strand	C9QYM3
5	50S ribosomal protein L1	protein	234	26% helix, 17% strand	H0QFK1
6	50S ribosomal protein L34	protein	46	35% helix, 0% strand	C9QXD2
7	50S ribosomal protein L35	protein	64	19% helix, 9% strand	C9QTZ0
8	50S ribosomal protein L36	protein	38	8% helix, 21% strand	C9QXI3
C	50S ribosomal protein L2	protein	271	4% helix, 23% strand	C9QXG5
F	50S ribosomal protein L5	protein	178	20% helix, 11% strand	C9QXH4
G	50S ribosomal protein L6	protein	175	17% helix, 26% strand	C9QXH7
H	50S ribosomal protein L9	protein	149	22% helix, 9% strand	C9QTM2
I	50S ribosomal protein L11	protein	141	28% helix, 12% strand	C9QV94
J	50S ribosomal protein L13	protein	142	23% helix, 13% strand	C9QXP2

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	1080	0.88	0.91	128	empty
2	908	0.88	0.91	68	empty
3	808	0.87	0.91	73	empty
4	804	0.86	0.90	83	empty
5	754	0.86	0.90	79	empty

Interfaces

63 interfaces between chains.

B–C · 6285 Å² buried · 173 hydrogen bonds · protein-nucleic
B–D · 4747 Å² buried · 131 hydrogen bonds · protein-nucleic
B–L · 4234 Å² buried · 125 hydrogen bonds · protein-nucleic
B–E · 4132 Å² buried · 111 hydrogen bonds · protein-nucleic
B–Q · 3940 Å² buried · 102 hydrogen bonds · protein-nucleic

Compared structures

3J8G · Electron cryo-microscopy structure of EngA bound with the 50S ribosomal subunit · 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 C9QUM4
Every structure of UniProt C9QXH2
Every structure of UniProt P02413
Every structure of UniProt C9QXH0
Every structure of UniProt C9QXG9
Every structure of UniProt C9QXI8
Every structure of UniProt C9QXH8
Every structure of UniProt C9R119
Every structure of UniProt C9QTZ1
Every structure of UniProt C9QY61
Every structure of UniProt C9QXG7
Every structure of UniProt C9QXG2
Every structure of UniProt B1X6G9
Every structure of UniProt C9QXI0
Every structure of UniProt C9QXH3
Every structure of UniProt C9QRC1
Every structure of UniProt C9QPR2
Every structure of UniProt C9QXG3
Every structure of UniProt C9QY62
Every structure of UniProt C9QYM3
Every structure of UniProt H0QFK1
Every structure of UniProt C9QXD2
Every structure of UniProt C9QTZ0
Every structure of UniProt C9QXI3
Every structure of UniProt C9QXG5
Every structure of UniProt C9QXH4
Every structure of UniProt C9QXH7
Every structure of UniProt C9QTM2
Every structure of UniProt C9QV94
Every structure of UniProt C9QXP2
Elsewhere: RCSB PDB 3J8G · PDBe 3J8G · UniProt C9QUM4 · UniProt C9QXH2 · UniProt P02413 · UniProt C9QXH0 · UniProt C9QXG9 · UniProt C9QXI8 · UniProt C9QXH8 · UniProt C9R119 · UniProt C9QTZ1 · UniProt C9QY61 · UniProt C9QXG7 · UniProt C9QXG2 · UniProt B1X6G9 · UniProt C9QXI0 · UniProt C9QXH3 · UniProt C9QRC1 · UniProt C9QPR2 · UniProt C9QXG3 · UniProt C9QY62 · UniProt C9QYM3 · UniProt H0QFK1 · UniProt C9QXD2 · UniProt C9QTZ0 · UniProt C9QXI3 · UniProt C9QXG5 · UniProt C9QXH4 · UniProt C9QXH7 · UniProt C9QTM2 · UniProt C9QV94 · UniProt C9QXP2

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