MolNFT v1 · #140050 · protein + RNA

Small subunit of trichomonas vaginalis ribosome

5XYI · 18S: “Small subunit of trichomonas vaginalis ribosome”. Electron microscopy, 20 pockets (best druggability 0.89). MolNFT v1 #140050 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5XYI
Type: protein + RNA
Length: 5,858 residues
Chains: 34
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 18S; 40S ribosomal protein sa; Ribosomal protein S3AE, putative; Uncharacterized protein…
UniProt: A2EFE7, A2G9Z8, A2EHK3, A2DIM3, A2FC75, A2E4S6, A2DEJ9, A2G5X6, A2E1L5, A2DNY3, A2EBA2, A2DHU8, A2FA40, A2D9L2, Q76KS8, A2DVD8, A2D919, A2DPS3, A2DTR8, A2EG54, A2FDE0, A2FFS8, A2DLW4, A2D895, A2F0H5, A2ER97, A2DST7, A2FBZ2, A2DQN8, A2DYA8, A2FHY5, A2ELV7
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 34 distinct chains · 29% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
2	18S	rna	1490	—	—
A	40S ribosomal protein sa	protein	204	34% helix, 9% strand	A2EFE7
B	Ribosomal protein S3AE, putative	protein	219	31% helix, 25% strand	A2G9Z8
C	Uncharacterized protein	protein	217	31% helix, 19% strand	A2EHK3
D	Ribosomal protein S3, putative	protein	208	36% helix, 24% strand	A2DIM3
E	40S ribosomal protein S4	protein	246	9% helix, 27% strand	A2FC75
F	40S ribosomal protein S5-B, putative	protein	186	52% helix, 6% strand	A2E4S6
G	40S ribosomal protein S6	protein	31	87% helix, 0% strand	A2DEJ9
H	40S ribosomal protein S7, putative	protein	163	29% helix, 21% strand	A2G5X6
I	40S ribosomal protein S8	protein	166	21% helix, 24% strand	A2E1L5
J	Uncharacterized protein	protein	162	52% helix, 3% strand	A2DNY3
K	PLECTIN/S10 domain containing protein	protein	90	42% helix, 21% strand	A2EBA2
L	Uncharacterized protein	protein	142	3% helix, 30% strand	A2DHU8
M	Ribosomal protein L7AE, putative	protein	103	39% helix, 12% strand	A2FA40
N	40S ribosomal protein S13, putative	protein	150	53% helix, 0% strand	A2D9L2
O	Ribosomal protein S14	protein	135	24% helix, 21% strand	Q76KS8
P	Ribosomal protein S19, putative	protein	118	37% helix, 13% strand	A2DVD8
Q	40S ribosomal protein S16, putative	protein	133	36% helix, 20% strand	A2D919
R	40S ribosomal protein S17-B, putative	protein	118	53% helix, 2% strand	A2DPS3
S	Ribosomal protein S13P/S18E, putative	protein	135	36% helix, 3% strand	A2DTR8
T	Ribosomal protein S19E, putative	protein	146	42% helix, 8% strand	A2EG54
U	Ribosomal protein S10P/S20E, putative	protein	97	26% helix, 35% strand	A2FDE0
V	40S ribosomal protein S21	protein	87	21% helix, 21% strand	A2FFS8
W	Ribosomal protein S15A	protein	128	30% helix, 21% strand	A2DLW4
X	40S ribosomal protein S23, putative	protein	140	21% helix, 24% strand	A2D895
Y	Ribosomal protein S24E, putative	protein	105	32% helix, 30% strand	A2F0H5
Z	Uncharacterized protein	protein	73	42% helix, 10% strand	A2ER97
a	40S ribosomal protein S26	protein	100	10% helix, 21% strand	A2DST7
b	40S ribosomal protein S27	protein	82	7% helix, 18% strand	A2FBZ2
c	Uncharacterized protein	protein	61	0% helix, 49% strand	A2DQN8
d	40S ribosomal protein S29, putative	protein	52	17% helix, 12% strand	A2DYA8
e	40S ribosomal protein S30	protein	42	40% helix, 0% strand	A2FHY5
g	Guanine nucleotide-binding protein beta subunit, putative	protein	305	0% helix, 48% strand	A2ELV7
n	EL41	protein	24	83% helix, 0% strand	—

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	989	0.89	0.91	121	empty
2	974	0.88	0.90	77	empty
3	931	0.87	0.90	103	empty
4	1192	0.87	0.89	126	empty
5	659	0.87	0.92	84	empty

Interfaces

87 interfaces between chains.

2–E · 3836 Å² buried · 60 hydrogen bonds · protein-nucleic
2–I · 3572 Å² buried · 72 hydrogen bonds · protein-nucleic
2–X · 3407 Å² buried · 64 hydrogen bonds · protein-nucleic
2–N · 3352 Å² buried · 63 hydrogen bonds · protein-nucleic
2–L · 2972 Å² buried · 56 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5XYI · Small subunit of Trichomonas vaginalis ribosome · the same entry in another collection · chain A against A, 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 A2EFE7
Every structure of UniProt A2G9Z8
Every structure of UniProt A2EHK3
Every structure of UniProt A2DIM3
Every structure of UniProt A2FC75
Every structure of UniProt A2E4S6
Every structure of UniProt A2DEJ9
Every structure of UniProt A2G5X6
Every structure of UniProt A2E1L5
Every structure of UniProt A2DNY3
Every structure of UniProt A2EBA2
Every structure of UniProt A2DHU8
Every structure of UniProt A2FA40
Every structure of UniProt A2D9L2
Every structure of UniProt Q76KS8
Every structure of UniProt A2DVD8
Every structure of UniProt A2D919
Every structure of UniProt A2DPS3
Every structure of UniProt A2DTR8
Every structure of UniProt A2EG54
Every structure of UniProt A2FDE0
Every structure of UniProt A2FFS8
Every structure of UniProt A2DLW4
Every structure of UniProt A2D895
Every structure of UniProt A2F0H5
Every structure of UniProt A2ER97
Every structure of UniProt A2DST7
Every structure of UniProt A2FBZ2
Every structure of UniProt A2DQN8
Every structure of UniProt A2DYA8
Every structure of UniProt A2FHY5
Every structure of UniProt A2ELV7
Elsewhere: RCSB PDB 5XYI · PDBe 5XYI · UniProt A2EFE7 · UniProt A2G9Z8 · UniProt A2EHK3 · UniProt A2DIM3 · UniProt A2FC75 · UniProt A2E4S6 · UniProt A2DEJ9 · UniProt A2G5X6 · UniProt A2E1L5 · UniProt A2DNY3 · UniProt A2EBA2 · UniProt A2DHU8 · UniProt A2FA40 · UniProt A2D9L2 · UniProt Q76KS8 · UniProt A2DVD8 · UniProt A2D919 · UniProt A2DPS3 · UniProt A2DTR8 · UniProt A2EG54 · UniProt A2FDE0 · UniProt A2FFS8 · UniProt A2DLW4 · UniProt A2D895 · UniProt A2F0H5 · UniProt A2ER97 · UniProt A2DST7 · UniProt A2FBZ2 · UniProt A2DQN8 · UniProt A2DYA8 · UniProt A2FHY5 · UniProt A2ELV7

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