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Cryo-EM structure of the 50S ribosomal subunit at 2.58 ångströms with modeled gbc secm peptide

Analyse Cryo-EM structure of the 50S ribosomal subunit at 2.58 ångströms with modeled… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YS3
Type: protein + RNA
Length: 6,217 residues
Chains: 32
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: A0A140N3L9, A0A140N7F5, A0A140N7G4, A0A140NAZ2, A0A140N5Z7, A0A140NHV0, A0A140N9E3, A0A140N5M6, A0A140N7J1, A0A140N3G7, A0A140N5K8, A0A140N5A3, A0A140N2T1, A0A140NDV1, A0A140N598, A0A140N3H4, A0A140N711, A0A140N6Z2, A0A140N4M0, A0A140N4L0, A0A140N6T7, A0A140NBS1, A0A140N5D7, A0A140N2S3, C6EGE8, A0A140N5L7, A0A140N846, A0A140N340, P02526
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 32 distinct chains · 22% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	50S ribosomal protein L28	protein	77	25% helix, 36% strand	A0A140N3L9
1	50S ribosomal protein L29	protein	61	74% helix, 0% strand	A0A140N7F5
2	50S ribosomal protein L30	protein	57	33% helix, 21% strand	A0A140N7G4
3	50S ribosomal protein L32	protein	55	13% helix, 15% strand	A0A140NAZ2
4	50S ribosomal protein L33	protein	50	0% helix, 46% strand	A0A140N5Z7
6	50S ribosomal protein L34	protein	46	52% helix, 0% strand	A0A140NHV0
7	50S ribosomal protein L35	protein	64	20% helix, 13% strand	A0A140N9E3
8	50S ribosomal protein L36	protein	38	8% helix, 47% strand	A0A140N5M6
a	5S rRNA	rna	118	—	—
b	23S rRNA	rna	2888	—	—
c	50S ribosomal protein L2	protein	271	5% helix, 29% strand	A0A140N7J1
d	50S ribosomal protein L3	protein	209	10% helix, 35% strand	A0A140N3G7
e	50S ribosomal protein L4	protein	201	30% helix, 10% strand	A0A140N5K8
f	50S ribosomal protein L5	protein	177	25% helix, 19% strand	A0A140N5A3
g	50S ribosomal protein L6	protein	176	15% helix, 28% strand	A0A140N2T1
h	50S ribosomal protein L9	protein	39	10% helix, 26% strand	A0A140NDV1
j	50S ribosomal protein L13	protein	142	33% helix, 19% strand	A0A140N598
k	50S ribosomal protein L14	protein	122	6% helix, 38% strand	A0A140N3H4
l	50S ribosomal protein L15	protein	143	14% helix, 11% strand	A0A140N711
m	50S ribosomal protein L16	protein	136	19% helix, 28% strand	A0A140N6Z2
n	50S ribosomal protein L17	protein	120	43% helix, 17% strand	A0A140N4M0
o	50S ribosomal protein L18	protein	116	37% helix, 20% strand	A0A140N4L0
p	50S ribosomal protein L19	protein	113	10% helix, 44% strand	A0A140N6T7
q	50S ribosomal protein L20	protein	117	77% helix, 0% strand	A0A140NBS1
r	50S ribosomal protein L21	protein	99	0% helix, 58% strand	A0A140N5D7
s	50S ribosomal protein L22	protein	109	37% helix, 39% strand	A0A140N2S3
t	50S ribosomal protein L23	protein	93	24% helix, 33% strand	C6EGE8
u	50S ribosomal protein L24	protein	102	3% helix, 46% strand	A0A140N5L7
v	Glycine-tRNA glyt	rna	75	—	—
w	50S ribosomal protein L25	protein	94	14% helix, 46% strand	A0A140N846
y	50S ribosomal protein L27	protein	74	0% helix, 38% strand	A0A140N340
z	Gamma-crystallin B	protein	35	11% helix, 0% strand	P02526

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	1062	0.89	0.91	105	empty
2	786	0.88	0.92	101	empty
3	1150	0.88	0.90	110	empty
4	876	0.87	0.91	78	empty
5	899	0.87	0.90	103	empty

Interfaces

63 interfaces between chains.

b–c · 7157 Å² buried · 172 hydrogen bonds · protein-nucleic
b–d · 5113 Å² buried · 121 hydrogen bonds · protein-nucleic
b–l · 4578 Å² buried · 112 hydrogen bonds · protein-nucleic
b–e · 4228 Å² buried · 90 hydrogen bonds · protein-nucleic
b–q · 4137 Å² buried · 100 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

6YS3 · Cryo-EM structure of the 50S ribosomal subunit at 2.58 Angstroms with modeled GBC SecM… · the same entry in another collection · chain 0 against 0, 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 A0A140N3L9
Every structure of UniProt A0A140N7F5
Every structure of UniProt A0A140N7G4
Every structure of UniProt A0A140NAZ2
Every structure of UniProt A0A140N5Z7
Every structure of UniProt A0A140NHV0
Every structure of UniProt A0A140N9E3
Every structure of UniProt A0A140N5M6
Every structure of UniProt A0A140N7J1
Every structure of UniProt A0A140N3G7
Every structure of UniProt A0A140N5K8
Every structure of UniProt A0A140N5A3
Every structure of UniProt A0A140N2T1
Every structure of UniProt A0A140NDV1
Every structure of UniProt A0A140N598
Every structure of UniProt A0A140N3H4
Every structure of UniProt A0A140N711
Every structure of UniProt A0A140N6Z2
Every structure of UniProt A0A140N4M0
Every structure of UniProt A0A140N4L0
Every structure of UniProt A0A140N6T7
Every structure of UniProt A0A140NBS1
Every structure of UniProt A0A140N5D7
Every structure of UniProt A0A140N2S3
Every structure of UniProt C6EGE8
Every structure of UniProt A0A140N5L7
Every structure of UniProt A0A140N846
Every structure of UniProt A0A140N340
Every structure of UniProt P02526
Elsewhere: RCSB PDB 6YS3 · PDBe 6YS3 · UniProt A0A140N3L9 · UniProt A0A140N7F5 · UniProt A0A140N7G4 · UniProt A0A140NAZ2 · UniProt A0A140N5Z7 · UniProt A0A140NHV0 · UniProt A0A140N9E3 · UniProt A0A140N5M6 · UniProt A0A140N7J1 · UniProt A0A140N3G7 · UniProt A0A140N5K8 · UniProt A0A140N5A3 · UniProt A0A140N2T1 · UniProt A0A140NDV1 · UniProt A0A140N598 · UniProt A0A140N3H4 · UniProt A0A140N711 · UniProt A0A140N6Z2 · UniProt A0A140N4M0 · UniProt A0A140N4L0 · UniProt A0A140N6T7 · UniProt A0A140NBS1 · UniProt A0A140N5D7 · UniProt A0A140N2S3 · UniProt C6EGE8 · UniProt A0A140N5L7 · UniProt A0A140N846 · UniProt A0A140N340 · UniProt P02526

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