Research workbench

Structure of ksrp in context of trypanosoma cruzi 40S

Analyse Structure of ksrp in context of trypanosoma cruzi 40S in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OPT
Type: protein + RNA
Length: 6,925 residues
Chains: 35
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Activated protein kinase C receptor, putative; Ribosomal protein S29, putative; 40S…
UniProt: Q4DTN2, Q4CXR4, Q4DEK4, Q4DGZ5, Q4E093, Q4D5P4, Q4DTQ1, Q4E0Q3, Q4CUC7, Q4DC38, Q4DN73, Q4CYE4, Q4D7C8, Q4D6I5, Q4DZ41, Q4D0U7, Q4DW38, Q4DU83, Q4D4S1, Q4CQ63, Q4DIZ9, Q4E0N6, Q4E3M0, Q4DTX6, Q4CSL1, Q4D1T6, Q4DSU0, Q4DK40, Q4D6H7, Q4DMK9, Q4E088, Q4DJY1, Q4DA48, Q4DY32
Pockets: 20 · best druggability 0.89

Structure

electron microscopy · 35 distinct chains · 27% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
p	Activated protein kinase C receptor, putative	protein	310	1% helix, 36% strand	Q4DTN2
q	Ribosomal protein S29, putative	protein	38	8% helix, 3% strand	Q4CXR4
r	40S ribosomal protein S16, putative	protein	140	34% helix, 19% strand	Q4DEK4
t	40S ribosomal protein S15, putative	protein	119	29% helix, 5% strand	Q4DGZ5
u	40S ribosomal protein S18, putative	protein	120	35% helix, 3% strand	Q4E093
L	40S ribosomal protein S4	protein	258	14% helix, 31% strand	Q4D5P4
M	40S ribosomal protein S23, putative	protein	142	23% helix, 25% strand	Q4DTQ1
O	40S ribosomal protein S5, putative	protein	190	42% helix, 5% strand	Q4E0Q3
Q	Ribosomal protein S7, putative	protein	200	38% helix, 19% strand	Q4CUC7
R	40S ribosomal protein S13, putative	protein	141	54% helix, 0% strand	Q4DC38
S	40S ribosomal protein S27, putative	protein	82	7% helix, 23% strand	Q4DN73
T	40S ribosomal protein S26	protein	104	19% helix, 13% strand	Q4CYE4
U	40S ribosomal protein S33, putative	protein	68	0% helix, 43% strand	Q4D7C8
V	40S ribosomal protein S14, putative	protein	135	22% helix, 22% strand	Q4D6I5
W	40S ribosomal protein S3A-2	protein	217	28% helix, 33% strand	Q4DZ41
X	40S ribosomal protein S11, putative	protein	148	5% helix, 28% strand	Q4D0U7
Y	40S ribosomal protein S24	protein	123	31% helix, 23% strand	Q4DW38
Z	40S ribosomal protein S8	protein	175	23% helix, 27% strand	Q4DU83
b	40S ribosomal protein S9, putative	protein	164	49% helix, 1% strand	Q4D4S1
f	40S ribosomal protein sa	protein	207	32% helix, 10% strand	Q4CQ63
d	40S ribosomal protein S2, putative	protein	223	30% helix, 24% strand	Q4DIZ9
e	40S ribosomal protein S15A, putative	protein	129	31% helix, 29% strand	Q4E0N6
g	40S ribosomal protein S21, putative	protein	83	13% helix, 23% strand	Q4E3M0
a	Ribosomal protein S25, putative	protein	70	41% helix, 11% strand	Q4DTX6
i	40S ribosomal protein S12	protein	121	41% helix, 15% strand	Q4CSL1
j	UBIQUITIN/RIBOSOMAL protein S27A, putative	protein	64	0% helix, 14% strand	Q4D1T6
P	40S ribosomal protein S6	protein	249	31% helix, 22% strand	Q4DSU0
k	40S ribosomal protein S17, putative	protein	118	53% helix, 2% strand	Q4DK40
l	Ribosomal protein S20, putative	protein	99	17% helix, 24% strand	Q4D6H7
m	40S ribosomal protein S3, putative	protein	200	37% helix, 23% strand	Q4DMK9
n	40S ribosomal protein S10, putative	protein	93	37% helix, 17% strand	Q4E088
o	Ribosomal protein S19, putative	protein	140	31% helix, 0% strand	Q4DJY1
c	40S ribosomal protein S30	protein	60	25% helix, 0% strand	Q4DA48
h	RNA-binding protein, putative	protein	173	28% helix, 16% strand	Q4DY32
E	18S rRNA	rna	2022	—	—

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	1178	0.89	0.91	102	empty
2	1025	0.88	0.90	69	empty
3	921	0.88	0.91	90	empty
4	956	0.87	0.90	78	empty
5	1044	0.87	0.89	100	empty

Interfaces

93 interfaces between chains.

P–E · 6306 Å² buried · 137 hydrogen bonds · protein-nucleic
Z–E · 4411 Å² buried · 113 hydrogen bonds · protein-nucleic
L–E · 4404 Å² buried · 84 hydrogen bonds · protein-nucleic
o–E · 3875 Å² buried · 91 hydrogen bonds · protein-nucleic
R–E · 3634 Å² buried · 83 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5OPT · Structure of KSRP in context of Trypanosoma cruzi 40S · the same entry in another collection · chain p against p, 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 Q4DTN2
Every structure of UniProt Q4CXR4
Every structure of UniProt Q4DEK4
Every structure of UniProt Q4DGZ5
Every structure of UniProt Q4E093
Every structure of UniProt Q4D5P4
Every structure of UniProt Q4DTQ1
Every structure of UniProt Q4E0Q3
Every structure of UniProt Q4CUC7
Every structure of UniProt Q4DC38
Every structure of UniProt Q4DN73
Every structure of UniProt Q4CYE4
Every structure of UniProt Q4D7C8
Every structure of UniProt Q4D6I5
Every structure of UniProt Q4DZ41
Every structure of UniProt Q4D0U7
Every structure of UniProt Q4DW38
Every structure of UniProt Q4DU83
Every structure of UniProt Q4D4S1
Every structure of UniProt Q4CQ63
Every structure of UniProt Q4DIZ9
Every structure of UniProt Q4E0N6
Every structure of UniProt Q4E3M0
Every structure of UniProt Q4DTX6
Every structure of UniProt Q4CSL1
Every structure of UniProt Q4D1T6
Every structure of UniProt Q4DSU0
Every structure of UniProt Q4DK40
Every structure of UniProt Q4D6H7
Every structure of UniProt Q4DMK9
Every structure of UniProt Q4E088
Every structure of UniProt Q4DJY1
Every structure of UniProt Q4DA48
Every structure of UniProt Q4DY32
Elsewhere: RCSB PDB 5OPT · PDBe 5OPT · UniProt Q4DTN2 · UniProt Q4CXR4 · UniProt Q4DEK4 · UniProt Q4DGZ5 · UniProt Q4E093 · UniProt Q4D5P4 · UniProt Q4DTQ1 · UniProt Q4E0Q3 · UniProt Q4CUC7 · UniProt Q4DC38 · UniProt Q4DN73 · UniProt Q4CYE4 · UniProt Q4D7C8 · UniProt Q4D6I5 · UniProt Q4DZ41 · UniProt Q4D0U7 · UniProt Q4DW38 · UniProt Q4DU83 · UniProt Q4D4S1 · UniProt Q4CQ63 · UniProt Q4DIZ9 · UniProt Q4E0N6 · UniProt Q4E3M0 · UniProt Q4DTX6 · UniProt Q4CSL1 · UniProt Q4D1T6 · UniProt Q4DSU0 · UniProt Q4DK40 · UniProt Q4D6H7 · UniProt Q4DMK9 · UniProt Q4E088 · UniProt Q4DJY1 · UniProt Q4DA48 · UniProt Q4DY32

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