Research workbench

Structure of the wild-type tel-SAM polymer

Analyse Structure of the wild-type tel-SAM polymer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1LKY
Type: protein
Length: 462 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transcription factor ETV6
UniProt: P41212
Ligands: SO4
Pockets: 4 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains · 59% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Transcription factor ETV6	protein	77	61% helix, 0% strand	P41212
B, D, F	Transcription factor ETV6	protein	77	57% helix, 0% strand	P41212

Ligands and binding sites

SO4 · Sulfate ion · ion · 11 copies · chains A, C, D, B, E, F

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	135	0.44	0.77	20	SO4
2	81	0.41	0.78	17	empty
3	142	0.40	0.74	21	empty
4	87	0.34	0.74	20	SO4

Interfaces

6 interfaces between chains.

A–B · 710 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 700 Å² buried · 17 hydrogen bonds · protein-protein
C–D · 674 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 454 Å² buried · 7 hydrogen bonds · protein-protein
A–D · 249 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1LKY · Structure of the wild-type TEL-SAM polymer · the same entry in another collection · chain F against F, TM-score 1.00
P41212 · AlphaFold monomer V2.0 prediction for transcription factor ETV6 (P41212) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 P41212
Elsewhere: RCSB PDB 1LKY · PDBe 1LKY · UniProt P41212

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