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Crystal structure of dimethylated rsl, cucurbituril-free form

Analyse Crystal structure of dimethylated rsl, cucurbituril-free form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6F7Y
Type: protein
Length: 357 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fucose-binding lectin protein
UniProt: A0A0S4TLR1
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 65% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fucose-binding lectin protein	protein	90	0% helix, 67% strand	A0A0S4TLR1
B, C, D	Fucose-binding lectin protein	protein	89	0% helix, 63% strand	A0A0S4TLR1

Ligands and binding sites

GOL · Glycerol · additive · 9 copies · chains A, B, D, C

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	619	0.75	0.82	69	empty
2	281	0.66	0.82	46	GOL
3	113	0.39	0.75	20	GOL

Interfaces

4 interfaces between chains.

B–C · 774 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 773 Å² buried · 12 hydrogen bonds · protein-protein
B–D · 770 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 680 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 modified (methylation, nonstandard).

Compared structures

6F7Y · Crystal structure of dimethylated RSL, cucurbituril-free form · 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 A0A0S4TLR1
Elsewhere: RCSB PDB 6F7Y · PDBe 6F7Y · UniProt A0A0S4TLR1

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