MolNFT v1 · #117870 · protein

Structure of the kh domain of T-star

5EL3 · Kh domain-containing, RNA-binding, signal transduction…: “Structure of the kh domain of T-star”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.67). MolNFT v1 #117870 on GenesisL1: 3D structure, binding sites and…

PDB: 5EL3
Type: protein
Length: 447 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kh domain-containing, RNA-binding, signal transduction- associated protein 3
UniProt: O75525
Ligands: SO4
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kh domain-containing, RNA-binding, signal transduction- associated protein 3	protein	108	46% helix, 19% strand	O75525
B, C, D	Kh domain-containing, RNA-binding, signal transduction- associated protein 3	protein	113	45% helix, 19% strand	O75525

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1086	0.67	0.73	96	empty
2	90	0.33	0.73	25	empty
3	69	0.32	0.75	16	empty
4	62	0.29	0.74	16	empty

Interfaces

4 interfaces between chains.

C–D · 900 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 670 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 519 Å² buried · 1 hydrogen bond · protein-protein
A–D · 466 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 16 modified (engineered).

Compared structures

5EL3 · Structure of the KH domain of T-STAR · the same entry in another collection · chain A against A, 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 B against A, TM-score 0.93

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 5EL3 · PDBe 5EL3 · UniProt O75525

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