MolNFT v1 · #135462 · protein + RNA

Architecture of the yeast small subunit processome

5TZS · 5' external transcribed spacer: “Architecture of the yeast small subunit processome”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #135462 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5TZS
Type: protein + RNA
Length: 17,017 residues
Chains: 58
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5' external transcribed spacer; 18S ribosomal RNA; U3 snorna; RPS6_ES6; RPS4_ES4…
EC: 2.1.1.260
UniProt: P0CX37, P0CX35, P26783, P26786, P0CX39, O13516, P0CX51, P0CX47, P0C0W1, P0CX31, Q3E7X9, Q06078, P39990, Q06506, Q08096, Q08965, Q06287, P0CX29
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 58 distinct chains · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
0	5' external transcribed spacer	rna	364	—	—
1	18S ribosomal RNA	rna	515	—	—
2	U3 snorna	rna	126	—	—
3	RPS6_ES6	protein	216	26% helix, 26% strand	P0CX37
5	RPS4_ES4	protein	241	17% helix, 32% strand	P0CX35
6	RPS5_US7	protein	202	47% helix, 3% strand	P26783
7	RPS7_ES7	protein	186	34% helix, 21% strand	P26786
8	RPS8_ES8	protein	173	26% helix, 27% strand	P0CX39
9	RPS9_US4	protein	185	51% helix, 3% strand	O13516
A	5' domain-associated	rna	39	—	—
B	3' domain-associated	rna	108	—	—
C	RPS16_US9	protein	115	43% helix, 25% strand	P0CX51
D	RPS11_US17	protein	146	3% helix, 32% strand	P0CX47
E	RPS22_US8	protein	127	35% helix, 27% strand	P0C0W1
F	RPS24_ES24	protein	90	22% helix, 37% strand	P0CX31
G	RPS28_ES28	protein	62	0% helix, 37% strand	Q3E7X9
H	UTP4	protein	544	0% helix, 51% strand	—
I	UTPA_CTD1	protein	176	84% helix, 0% strand	—
J	UTPA_CTD2	protein	107	84% helix, 0% strand	—
K	UTPA_CTD2	protein	105	87% helix, 0% strand	—
M	Beta-propeller 2	protein	258	0% helix, 46% strand	—
N	UTP17	protein	545	0% helix, 47% strand	—
O	UTP1	protein	638	15% helix, 38% strand	—
P	UTP6	protein	306	85% helix, 0% strand	—
Q	UTP12	protein	710	15% helix, 34% strand	—
R	UTP13	protein	717	17% helix, 40% strand	—
S	UTP18	protein	250	0% helix, 45% strand	—
T	UTP21	protein	749	13% helix, 43% strand	Q06078
U	Beta-propeller 5	protein	284	0% helix, 55% strand	—
V	ENP2	protein	263	0% helix, 56% strand	—
W	UTPA_CTD4	protein	104	87% helix, 0% strand	—
X	KRE33	protein	640	41% helix, 15% strand	—
Y	KRE33	protein	641	40% helix, 15% strand	—
Z	IMP3	protein	151	54% helix, 4% strand	—
a	NOP56	protein	312	57% helix, 4% strand	—
b	NOP58	protein	341	60% helix, 7% strand	—
c	NOP1	protein	221	27% helix, 30% strand	—
d	NOP1	protein	216	29% helix, 21% strand	—
e	SNU13	protein	122	50% helix, 16% strand	P39990
f	SNU13	protein	114	54% helix, 17% strand	P39990
g	Ribosomal RNA-processing protein 9	protein	365	2% helix, 46% strand	Q06506
h	RNA 3'-terminal phosphate cyclase-like protein	protein	355	30% helix, 28% strand	Q08096
i	BMS1,RIBOSOME biogenesis protein BMS1,BMS1	protein	475	20% helix, 30% strand	Q08965
j	Ribosomal RNA small subunit methyltransferase NEP1 (EC 2.1.1.260)	protein	211	31% helix, 24% strand	Q06287
k	Ribosomal RNA small subunit methyltransferase NEP1 (EC 2.1.1.260)	protein	218	30% helix, 23% strand	Q06287
l	UTP24	protein	124	40% helix, 14% strand	—
m	IMP4	protein	156	22% helix, 31% strand	—
n	UTP30	protein	160	46% helix, 6% strand	—
o	Unassigned kh domain	protein	173	53% helix, 20% strand	—
p	UTP20	protein	924	88% helix, 0% strand	—
q	Repeat protein 2	protein	372	87% helix, 0% strand	—
r	40S ribosomal protein S23-a	protein	82	12% helix, 28% strand	P0CX29
s	Beta-propeller 1	protein	290	0% helix, 31% strand	—
t	Beta-propeller 1	protein	269	0% helix, 34% strand	—
u	Beta-propeller 1	protein	274	0% helix, 47% strand	—
v	Repeat protein 1	protein	577	89% helix, 0% strand	—
y	Unassigned protein helices	protein	507	92% helix, 0% strand	—
z	Unassigned RNA helices	rna	76	—	—

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	1529	0.86	0.87	203	empty
2	1285	0.84	0.85	140	empty
3	2166	0.82	0.83	237	empty
4	2168	0.81	0.83	247	empty
5	875	0.81	0.84	57	empty

Interfaces

133 interfaces between chains.

1–8 · 1902 Å² buried · 47 hydrogen bonds · protein-nucleic
1–3 · 1813 Å² buried · 48 hydrogen bonds · protein-nucleic
1–D · 1130 Å² buried · 25 hydrogen bonds · protein-nucleic
1–5 · 949 Å² buried · 27 hydrogen bonds · protein-nucleic
h–i · 765 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

5TZS · Architecture of the yeast small subunit processome · the same entry in another collection · chain D against D, 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 P0CX37
Every structure of UniProt P0CX35
Every structure of UniProt P26783
Every structure of UniProt P26786
Every structure of UniProt P0CX39
Every structure of UniProt O13516
Every structure of UniProt P0CX51
Every structure of UniProt P0CX47
Every structure of UniProt P0C0W1
Every structure of UniProt P0CX31
Every structure of UniProt Q3E7X9
Every structure of UniProt Q06078
Every structure of UniProt P39990
Every structure of UniProt Q06506
Every structure of UniProt Q08096
Every structure of UniProt Q08965
Every structure of UniProt Q06287
Every structure of UniProt P0CX29
Elsewhere: RCSB PDB 5TZS · PDBe 5TZS · UniProt P0CX37 · UniProt P0CX35 · UniProt P26783 · UniProt P26786 · UniProt P0CX39 · UniProt O13516 · UniProt P0CX51 · UniProt P0CX47 · UniProt P0C0W1 · UniProt P0CX31 · UniProt Q3E7X9 · UniProt Q06078 · UniProt P39990 · UniProt Q06506 · UniProt Q08096 · UniProt Q08965 · UniProt Q06287 · UniProt P0CX29

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