Research workbench

50S subunit with ef-G(GDPNP) and rrf bound

Analyse 50S subunit with ef-G(GDPNP) and rrf bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2RDO
Type: protein
Length: 4,470 residues
Chains: 32
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 50S ribosomal protein L25; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S…
UniProt: P68919, P60422, P60438, P60723, P62399, P0AG55, P0AA10, P0ADY3, P02413, P0ADY7, P0AG44, P0C018, P0A7K6, P0A7L3, P0AG48, P61175, P0ADZ0, P60624, P0A7L8, P0A7M6, P0AG51, P0A7M9, P0A7N4, P0A7N9, P0A7P5, P0A7Q1, P0A7Q6, P0A7J7, P0A7R1, P0A7L0, P0A6M8, P0A805
Pockets: 4 · best druggability 0.41

Structure

electron microscopy · 32 distinct chains · 0% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
V	50S ribosomal protein L25	protein	94	0% helix, 0% strand	P68919
C	50S ribosomal protein L2	protein	267	0% helix, 0% strand	P60422
D	50S ribosomal protein L3	protein	209	0% helix, 0% strand	P60438
E	50S ribosomal protein L4	protein	201	0% helix, 0% strand	P60723
F	50S ribosomal protein L5	protein	178	0% helix, 0% strand	P62399
G	50S ribosomal protein L6	protein	176	0% helix, 0% strand	P0AG55
J	50S ribosomal protein L13	protein	140	0% helix, 0% strand	P0AA10
K	50S ribosomal protein L14	protein	121	0% helix, 0% strand	P0ADY3
L	50S ribosomal protein L15	protein	144	0% helix, 0% strand	P02413
M	50S ribosomal protein L16	protein	136	0% helix, 0% strand	P0ADY7
N	50S ribosomal protein L17	protein	127	0% helix, 0% strand	P0AG44
O	50S ribosomal protein L18	protein	117	0% helix, 0% strand	P0C018
P	50S ribosomal protein L19	protein	114	0% helix, 0% strand	P0A7K6
Q	50S ribosomal protein L20	protein	117	0% helix, 0% strand	P0A7L3
R	50S ribosomal protein L21	protein	103	0% helix, 0% strand	P0AG48
S	50S ribosomal protein L22	protein	110	0% helix, 0% strand	P61175
T	50S ribosomal protein L23	protein	99	0% helix, 0% strand	P0ADZ0
U	50S ribosomal protein L24	protein	102	0% helix, 0% strand	P60624
W	50S ribosomal protein L27	protein	84	0% helix, 0% strand	P0A7L8
X	50S ribosomal protein L29	protein	63	0% helix, 0% strand	P0A7M6
Y	50S ribosomal protein L30	protein	58	0% helix, 0% strand	P0AG51
Z	50S ribosomal protein L31	protein	70	0% helix, 0% strand	P0A7M9
0	50S ribosomal protein L32	protein	56	0% helix, 0% strand	P0A7N4
1	50S ribosomal protein L33	protein	54	0% helix, 0% strand	P0A7N9
2	50S ribosomal protein L34	protein	46	0% helix, 0% strand	P0A7P5
3	50S ribosomal protein L35	protein	64	0% helix, 0% strand	P0A7Q1
4	50S ribosomal protein L36	protein	38	0% helix, 0% strand	P0A7Q6
I	50S ribosomal protein L11	protein	141	0% helix, 0% strand	P0A7J7
H	50S ribosomal protein L9	protein	149	0% helix, 0% strand	P0A7R1
9	50S ribosomal protein L1	protein	223	0% helix, 0% strand	P0A7L0
7	Elongation factor G	protein	684	0% helix, 0% strand	P0A6M8
8	Ribosome recycling factor	protein	185	0% helix, 0% strand	P0A805

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	117	0.41	0.73	29	empty
2	120	0.39	0.72	34	empty
3	78	0.33	0.73	25	empty
4	58	0.28	0.72	23	empty

Interfaces

6 interfaces between chains.

7–8 · 89 Å² buried · 0 hydrogen bonds · protein-protein
C–H · 64 Å² buried · 0 hydrogen bonds · protein-protein
E–L · 50 Å² buried · 0 hydrogen bonds · protein-protein
L–3 · 31 Å² buried · 0 hydrogen bonds · protein-protein
D–K · 21 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

2RDO · 50S subunit with EF-G(GDPNP) and RRF bound · the same entry in another collection · chain N against N, 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 P68919
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 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 P0A7L8
Every structure of UniProt P0A7M6
Every structure of UniProt P0AG51
Every structure of UniProt P0A7M9
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 P0A7J7
Every structure of UniProt P0A7R1
Every structure of UniProt P0A7L0
Every structure of UniProt P0A6M8
Every structure of UniProt P0A805
Elsewhere: RCSB PDB 2RDO · PDBe 2RDO · UniProt P68919 · UniProt P60422 · UniProt P60438 · UniProt P60723 · UniProt P62399 · UniProt P0AG55 · 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 P0A7L8 · UniProt P0A7M6 · UniProt P0AG51 · UniProt P0A7M9 · UniProt P0A7N4 · UniProt P0A7N9 · UniProt P0A7P5 · UniProt P0A7Q1 · UniProt P0A7Q6 · UniProt P0A7J7 · UniProt P0A7R1 · UniProt P0A7L0 · UniProt P0A6M8 · UniProt P0A805

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