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Structure of the kh domain of T-star in complex with aaauaa RNA

Analyse Structure of the kh domain of T-star in complex with aaauaa RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5ELS
Type: protein + RNA
Length: 684 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kh domain-containing, RNA-binding, signal transduction- associated protein 3; RNA…
UniProt: O75525
Ligands: SO4
Pockets: 9 · best druggability 0.75

Structure

x-ray diffraction · 5 distinct chains · 44% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Kh domain-containing, RNA-binding, signal transduction- associated protein 3	protein	113	47% helix, 19% strand	O75525
D	Kh domain-containing, RNA-binding, signal transduction- associated protein 3	protein	111	42% helix, 19% strand	O75525
E	Kh domain-containing, RNA-binding, signal transduction- associated protein 3	protein	110	45% helix, 19% strand	O75525
F	Kh domain-containing, RNA-binding, signal transduction- associated protein 3	protein	112	40% helix, 17% strand	O75525
H, I	RNA (5'-R(PAPAPAPUPAPA)-3')	rna	6	—	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1110	0.75	0.78	90	empty
2	470	0.59	0.74	48	empty
3	197	0.53	0.78	26	SO4
4	201	0.52	0.78	32	empty
5	51	0.32	0.77	18	empty

Interfaces

14 interfaces between chains.

D–E · 896 Å² buried · 9 hydrogen bonds · protein-protein
H–I · 810 Å² buried · 217 hydrogen bonds · nucleic-nucleic
C–I · 627 Å² buried · 9 hydrogen bonds · protein-nucleic
C–H · 555 Å² buried · 11 hydrogen bonds · protein-nucleic
A–H · 527 Å² buried · 12 hydrogen bonds · protein-nucleic

Compared structures

5ELS · Structure of the KH domain of T-STAR in complex with AAAUAA RNA · the same entry in another collection · chain I against I, TM-score 1.00
O75525 · AlphaFold monomer V2.0 prediction for kh domain-containing, RNA- binding, signal… · a predicted model of the same protein · chain E against A, TM-score 0.97

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 O75525
Elsewhere: RCSB PDB 5ELS · PDBe 5ELS · UniProt O75525

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