Research workbench

70S E. COLI ribosome with an extended UL23 loop from candidatus marinimicrobia

Analyse 70S E. COLI ribosome with an extended UL23 loop from candidatus marinimicrobia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7ZOD
Type: protein + RNA
Length: 6,209 residues
Chains: 31
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L28; 50S ribosomal protein L29; 50S ribosomal protein L30; 50S…
UniProt: P0A7M2, P0A7M6, P0AG51, P0A7N4, P0A7N9, P0A7P5, P0A7Q1, A0A2X1PTA3, P60422, P60438, P60723, P62399, P0AG55, P0A7R1, P0AA10, P0ADY3, P02413, A0A829G538, P0AG44, P0C018, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P68919, P0A7L8
Pockets: 20 · best druggability 0.88

Structure

electron microscopy · 31 distinct chains · 25% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	50S ribosomal protein L28	protein	77	26% helix, 36% strand	P0A7M2
1	50S ribosomal protein L29	protein	61	69% helix, 0% strand	P0A7M6
2	50S ribosomal protein L30	protein	57	33% helix, 21% strand	P0AG51
3	50S ribosomal protein L32	protein	55	15% helix, 16% strand	P0A7N4
4	50S ribosomal protein L33	protein	50	0% helix, 48% strand	P0A7N9
6	50S ribosomal protein L34	protein	46	59% helix, 0% strand	P0A7P5
7	50S ribosomal protein L35	protein	64	31% helix, 11% strand	P0A7Q1
8	50S ribosomal protein L36	protein	38	8% helix, 47% strand	A0A2X1PTA3
a	5S rRNA	rna	118	—	—
b	23S rRNA	rna	2901	—	—
c	50S ribosomal protein L2	protein	271	6% helix, 29% strand	P60422
d	50S ribosomal protein L3	protein	209	12% helix, 35% strand	P60438
e	50S ribosomal protein L4	protein	201	35% helix, 12% strand	P60723
f	50S ribosomal protein L5	protein	177	37% helix, 20% strand	P62399
g	50S ribosomal protein L6	protein	176	18% helix, 36% strand	P0AG55
h	50S ribosomal protein L9	protein	39	8% helix, 26% strand	P0A7R1
j	50S ribosomal protein L13	protein	142	32% helix, 19% strand	P0AA10
k	50S ribosomal protein L14	protein	122	7% helix, 38% strand	P0ADY3
l	50S ribosomal protein L15	protein	143	20% helix, 13% strand	P02413
m	50S ribosomal protein L16	protein	136	20% helix, 28% strand	A0A829G538
n	50S ribosomal protein L17	protein	120	44% helix, 17% strand	P0AG44
o	50S ribosomal protein L18	protein	116	41% helix, 18% strand	P0C018
p	50S ribosomal protein L19	protein	113	18% helix, 42% strand	P0A7K6
q	50S ribosomal protein L20	protein	117	79% helix, 0% strand	P0A7L3
r	50S ribosomal protein L21	protein	102	0% helix, 58% strand	P0AG48
s	50S ribosomal protein L22	protein	109	40% helix, 35% strand	P61175
t	50S ribosomal protein L23	protein	101	28% helix, 39% strand	P0ADZ0
u	50S ribosomal protein L24	protein	102	3% helix, 45% strand	P60624
v	Pro-tRNA	rna	77	—	—
w	50S ribosomal protein L25	protein	94	21% helix, 46% strand	P68919
y	50S ribosomal protein L27	protein	75	0% helix, 41% strand	P0A7L8

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	1107	0.88	0.90	100	empty
2	1020	0.87	0.89	89	empty
3	993	0.87	0.89	81	empty
4	854	0.84	0.88	64	empty
5	520	0.84	0.91	60	empty

Interfaces

60 interfaces between chains.

b–c · 7086 Å² buried · 178 hydrogen bonds · protein-nucleic
b–d · 5043 Å² buried · 103 hydrogen bonds · protein-nucleic
b–l · 4470 Å² buried · 102 hydrogen bonds · protein-nucleic
b–e · 4099 Å² buried · 83 hydrogen bonds · protein-nucleic
b–q · 4073 Å² buried · 96 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7ZOD · 70S E. coli ribosome with an extended uL23 loop from Candidatus marinimicrobia · the same entry in another collection · chain 1 against 1, 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 P0A7M2
Every structure of UniProt P0A7M6
Every structure of UniProt P0AG51
Every structure of UniProt P0A7N4
Every structure of UniProt P0A7N9
Every structure of UniProt P0A7P5
Every structure of UniProt P0A7Q1
Every structure of UniProt A0A2X1PTA3
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 P0AA10
Every structure of UniProt P0ADY3
Every structure of UniProt P02413
Every structure of UniProt A0A829G538
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
Elsewhere: RCSB PDB 7ZOD · PDBe 7ZOD · UniProt P0A7M2 · UniProt P0A7M6 · UniProt P0AG51 · UniProt P0A7N4 · UniProt P0A7N9 · UniProt P0A7P5 · UniProt P0A7Q1 · UniProt A0A2X1PTA3 · UniProt P60422 · UniProt P60438 · UniProt P60723 · UniProt P62399 · UniProt P0AG55 · UniProt P0A7R1 · UniProt P0AA10 · UniProt P0ADY3 · UniProt P02413 · UniProt A0A829G538 · UniProt P0AG44 · UniProt P0C018 · UniProt P0A7K6 · UniProt P0A7L3 · UniProt P0AG48 · UniProt P61175 · UniProt P0ADZ0 · UniProt P60624 · UniProt P68919 · UniProt P0A7L8

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