Research workbench

Yeast nucleolar pre-60S ribosomal subunit (state 3)

Analyse Yeast nucleolar pre-60S ribosomal subunit (state 3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6CB1
Type: protein + RNA
Length: 8,766 residues
Chains: 40
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 35S pre-ribosomal RNA miscrna; 5.8S rRNA; ITS2; Ribosome biogenesis protein NSA1; 60S…
EC: 3.6.4.13
UniProt: A0A250WFX4, A0A250WNS8, A0A250WFC2, A0A250WCF3, P17076, A0A250WKW9, A0A250WL31, A0A250W9H2, P36105, P05748, A0A250WM14, P05740, A0A250WH37, A0A250WE58, A0A250WBI4, P05743, P0C2H6, P40007, Q08235, P14120, A0A250WF67, P05744, A0A250WJC9, A0A250W9S3, P05745, P49166, A0A250WKJ9, P53927, A0A250WER3, A6ZMA9, Q04660, P40693, P35178
Ligands: ZN
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 40 distinct chains · 35% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	35S pre-ribosomal RNA miscrna	rna	1370	—	—
2	5.8S rRNA	rna	158	—	—
6	ITS2	rna	87	—	—
A	Ribosome biogenesis protein NSA1	protein	394	3% helix, 43% strand	—
C	60S ribosomal protein L4-a	protein	314	36% helix, 10% strand	A0A250WFX4
D	Protein MAK16	protein	190	47% helix, 14% strand	A0A250WNS8
E	60S ribosomal protein L6-a	protein	170	27% helix, 18% strand	A0A250WFC2
F	60S ribosomal protein L7-a	protein	242	52% helix, 11% strand	A0A250WCF3
G	60S ribosomal protein L8-a	protein	187	45% helix, 9% strand	P17076
I	Ribosome production factor 1	protein	288	31% helix, 27% strand	A0A250WKW9
K	Proteasome-interacting protein CIC1	protein	260	43% helix, 21% strand	A0A250WL31
L	60S ribosomal protein L13-a	protein	106	43% helix, 12% strand	A0A250W9H2
M	60S ribosomal protein L14-a	protein	128	42% helix, 24% strand	P36105
N	60S ribosomal protein L15-a	protein	176	41% helix, 19% strand	P05748
O	60S ribosomal protein L16-a	protein	184	60% helix, 14% strand	A0A250WM14
P	60S ribosomal protein L17-a	protein	124	35% helix, 27% strand	P05740
Q	60S ribosomal protein L18-a	protein	132	38% helix, 19% strand	A0A250WH37
S	60S ribosomal protein L20-a	protein	171	22% helix, 30% strand	A0A250WE58
X	60S ribosomal protein L25	protein	141	30% helix, 18% strand	A0A250WBI4
Y	60S ribosomal protein L26-a	protein	126	30% helix, 32% strand	P05743
Z	60S ribosomal protein L27-a	protein	135	22% helix, 28% strand	P0C2H6
7	Nucleolar protein 16	protein	156	40% helix, 1% strand	P40007
b	Ribosome biogenesis protein BRX1	protein	242	30% helix, 26% strand	Q08235
c	60S ribosomal protein L30	protein	97	46% helix, 15% strand	P14120
d	Ribosome biogenesis protein YTM1	protein	465	10% helix, 44% strand	—
e	60S ribosomal protein L32	protein	114	21% helix, 12% strand	A0A250WF67
f	60S ribosomal protein L33-a	protein	106	6% helix, 49% strand	P05744
g	60S ribosomal protein L34-a	protein	101	26% helix, 10% strand	A0A250WJC9
h	60S ribosomal protein L35-a	protein	119	60% helix, 3% strand	A0A250W9S3
i	60S ribosomal protein L36-a	protein	84	73% helix, 0% strand	P05745
j	60S ribosomal protein L37-a	protein	72	21% helix, 8% strand	P49166
k	60S ribosomal protein L38	protein	77	23% helix, 43% strand	A0A250WKJ9
m	RRNA-processing protein EBP2	protein	74	55% helix, 3% strand	—
n	Pescadillo homolog	protein	341	47% helix, 7% strand	—
o	Ribosome biogenesis protein 15	protein	133	29% helix, 26% strand	P53927
p	ATP-dependent RNA helicase HAS1 (EC 3.6.4.13)	protein	437	48% helix, 14% strand	A0A250WER3
s	Ribosome biogenesis protein ERB1	protein	512	18% helix, 32% strand	A6ZMA9, Q04660
t	Ribosome biogenesis protein RLP7	protein	282	47% helix, 14% strand	P40693
x	BRX1 associated peptide	protein	28	46% helix, 0% strand	—
z	Ribosomal RNA-processing protein 1	protein	243	77% helix, 0% strand	P35178

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains D, j

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	704	0.85	0.90	85	empty
2	1011	0.85	0.86	113	empty
3	1102	0.84	0.86	123	empty
4	500	0.83	0.91	86	empty
5	680	0.83	0.88	125	empty

Interfaces

131 interfaces between chains.

1–2 · 4692 Å² buried · 352 hydrogen bonds · nucleic-nucleic
1–C · 3920 Å² buried · 49 hydrogen bonds · protein-nucleic
1–N · 2033 Å² buried · 16 hydrogen bonds · protein-nucleic
1–g · 1819 Å² buried · 10 hydrogen bonds · protein-nucleic
6–K · 1626 Å² buried · 17 hydrogen bonds · protein-nucleic

Compared structures

6CB1 · Yeast nucleolar pre-60S ribosomal subunit (state 3) · the same entry in another collection · chain I against I, 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 A0A250WFX4
Every structure of UniProt A0A250WNS8
Every structure of UniProt A0A250WFC2
Every structure of UniProt A0A250WCF3
Every structure of UniProt P17076
Every structure of UniProt A0A250WKW9
Every structure of UniProt A0A250WL31
Every structure of UniProt A0A250W9H2
Every structure of UniProt P36105
Every structure of UniProt P05748
Every structure of UniProt A0A250WM14
Every structure of UniProt P05740
Every structure of UniProt A0A250WH37
Every structure of UniProt A0A250WE58
Every structure of UniProt A0A250WBI4
Every structure of UniProt P05743
Every structure of UniProt P0C2H6
Every structure of UniProt P40007
Every structure of UniProt Q08235
Every structure of UniProt P14120
Every structure of UniProt A0A250WF67
Every structure of UniProt P05744
Every structure of UniProt A0A250WJC9
Every structure of UniProt A0A250W9S3
Every structure of UniProt P05745
Every structure of UniProt P49166
Every structure of UniProt A0A250WKJ9
Every structure of UniProt P53927
Every structure of UniProt A0A250WER3
Every structure of UniProt A6ZMA9
Every structure of UniProt Q04660
Every structure of UniProt P40693
Every structure of UniProt P35178
Elsewhere: RCSB PDB 6CB1 · PDBe 6CB1 · UniProt A0A250WFX4 · UniProt A0A250WNS8 · UniProt A0A250WFC2 · UniProt A0A250WCF3 · UniProt P17076 · UniProt A0A250WKW9 · UniProt A0A250WL31 · UniProt A0A250W9H2 · UniProt P36105 · UniProt P05748 · UniProt A0A250WM14 · UniProt P05740 · UniProt A0A250WH37 · UniProt A0A250WE58 · UniProt A0A250WBI4 · UniProt P05743 · UniProt P0C2H6 · UniProt P40007 · UniProt Q08235 · UniProt P14120 · UniProt A0A250WF67 · UniProt P05744 · UniProt A0A250WJC9 · UniProt A0A250W9S3 · UniProt P05745 · UniProt P49166 · UniProt A0A250WKJ9 · UniProt P53927 · UniProt A0A250WER3 · UniProt A6ZMA9 · UniProt Q04660 · UniProt P40693 · UniProt P35178

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