MolNFT v1 · #144661 · protein + RNA

Yeast nucleolar pre-60S ribosomal subunit (state 2)

6C0F · Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA miscrna: “Yeast nucleolar pre-60S ribosomal subunit (state 2)”. Electron microscopy, 1 ligand (ZN), 20 pockets (best druggability 0.89). MolNFT v1 #144661 on GenesisL1: 3D…

PDB: 6C0F
Type: protein + RNA
Length: 8,925 residues
Chains: 43
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA miscrna; 5.8S rRNA; ITS2; Ribosome…
EC: 3.6.4.13
UniProt: P53136, P14126, P10664, P10962, Q02326, P05737, P17076, P38805, P38779, Q12690, P36105, P05748, P26784, P05740, P0CX49, P0CX23, P0CX41, Q02892, P05743, P40007, P36080, P38061, P05744, P0CX84, P05745, P49166, P53261, P53927, Q03532, P40693, Q07915, P38789, Q06511, Q12522, P35178
Ligands: ZN
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 43 distinct chains · 36% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
1	Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA miscrna	rna	1357	—	—
2	5.8S rRNA	rna	158	—	—
6	ITS2	rna	87	—	—
A	Ribosome biogenesis protein NSA1	protein	394	3% helix, 43% strand	P53136
B	60S ribosomal protein L3	protein	324	15% helix, 32% strand	P14126
C	60S ribosomal protein L4-a	protein	314	36% helix, 10% strand	P10664
D	Protein MAK16	protein	190	47% helix, 14% strand	P10962
E	60S ribosomal protein L6-a	protein	170	27% helix, 18% strand	Q02326
F	60S ribosomal protein L7-a	protein	242	52% helix, 11% strand	P05737
G	60S ribosomal protein L8-a	protein	187	45% helix, 9% strand	P17076
I	Ribosome production factor 1	protein	288	31% helix, 27% strand	P38805
K	Proteasome-interacting protein CIC1	protein	260	43% helix, 21% strand	P38779
L	60S ribosomal protein L13-a	protein	106	43% helix, 12% strand	Q12690
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	P26784
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	P0CX49
S	60S ribosomal protein L20-a	protein	171	22% helix, 30% strand	P0CX23
V	60S ribosomal protein L23-a	protein	122	9% helix, 42% strand	P0CX41
W	Nucleolar GTP-binding protein 1	protein	98	32% helix, 4% strand	Q02892
Y	60S ribosomal protein L26-a	protein	126	30% helix, 32% strand	P05743
7	Nucleolar protein 16	protein	156	40% helix, 1% strand	P40007
8	Ribosomal RNA-processing protein 14	protein	98	89% helix, 0% strand	P36080
b	Ribosome biogenesis protein BRX1	protein	242	30% helix, 26% strand	—
e	60S ribosomal protein L32	protein	114	21% helix, 12% strand	P38061
f	60S ribosomal protein L33-a	protein	106	6% helix, 49% strand	P05744
h	60S ribosomal protein L35-a	protein	119	60% helix, 3% strand	P0CX84
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
x	BRX1-associated peptide	protein	28	46% helix, 0% strand	—
m	RRNA-processing protein EBP2	protein	74	55% helix, 3% strand	—
n	Pescadillo homolog	protein	341	47% helix, 7% strand	P53261
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	Q03532
q	Protein MAK11	protein	285	0% helix, 52% strand	—
s	Ribosome biogenesis protein ERB1	protein	157	41% helix, 1% strand	—
t	Ribosome biogenesis protein RLP7	protein	248	42% helix, 15% strand	P40693
u	Ribosome biogenesis protein RLP24	protein	129	43% helix, 9% strand	Q07915
v	Ribosome biogenesis protein SSF1	protein	225	23% helix, 27% strand	P38789
w	Ribosomal RNA-processing protein 15	protein	70	84% helix, 0% strand	Q06511
y	Eukaryotic translation initiation factor 6	protein	226	24% helix, 23% strand	Q12522
z	Ribosomal RNA-processing protein 1	protein	243	77% helix, 0% strand	P35178

Ligands and binding sites

ZN · Zinc ion · metal · 3 copies · chains D, j, u

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	847	0.89	0.92	97	empty
2	1151	0.88	0.91	124	empty
3	750	0.88	0.92	74	empty
4	640	0.87	0.92	83	empty
5	978	0.87	0.88	92	empty

Interfaces

151 interfaces between chains.

1–C · 6989 Å² buried · 181 hydrogen bonds · protein-nucleic
1–B · 5292 Å² buried · 149 hydrogen bonds · protein-nucleic
1–N · 4546 Å² buried · 84 hydrogen bonds · protein-nucleic
1–2 · 4267 Å² buried · 333 hydrogen bonds · nucleic-nucleic
1–O · 3440 Å² buried · 75 hydrogen bonds · protein-nucleic

Compared structures

6C0F · Yeast nucleolar pre-60S ribosomal subunit (state 2) · 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 P53136
Every structure of UniProt P14126
Every structure of UniProt P10664
Every structure of UniProt P10962
Every structure of UniProt Q02326
Every structure of UniProt P05737
Every structure of UniProt P17076
Every structure of UniProt P38805
Every structure of UniProt P38779
Every structure of UniProt Q12690
Every structure of UniProt P36105
Every structure of UniProt P05748
Every structure of UniProt P26784
Every structure of UniProt P05740
Every structure of UniProt P0CX49
Every structure of UniProt P0CX23
Every structure of UniProt P0CX41
Every structure of UniProt Q02892
Every structure of UniProt P05743
Every structure of UniProt P40007
Every structure of UniProt P36080
Every structure of UniProt P38061
Every structure of UniProt P05744
Every structure of UniProt P0CX84
Every structure of UniProt P05745
Every structure of UniProt P49166
Every structure of UniProt P53261
Every structure of UniProt P53927
Every structure of UniProt Q03532
Every structure of UniProt P40693
Every structure of UniProt Q07915
Every structure of UniProt P38789
Every structure of UniProt Q06511
Every structure of UniProt Q12522
Every structure of UniProt P35178
Elsewhere: RCSB PDB 6C0F · PDBe 6C0F · UniProt P53136 · UniProt P14126 · UniProt P10664 · UniProt P10962 · UniProt Q02326 · UniProt P05737 · UniProt P17076 · UniProt P38805 · UniProt P38779 · UniProt Q12690 · UniProt P36105 · UniProt P05748 · UniProt P26784 · UniProt P05740 · UniProt P0CX49 · UniProt P0CX23 · UniProt P0CX41 · UniProt Q02892 · UniProt P05743 · UniProt P40007 · UniProt P36080 · UniProt P38061 · UniProt P05744 · UniProt P0CX84 · UniProt P05745 · UniProt P49166 · UniProt P53261 · UniProt P53927 · UniProt Q03532 · UniProt P40693 · UniProt Q07915 · UniProt P38789 · UniProt Q06511 · UniProt Q12522 · UniProt P35178

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