MolNFT v1 · #147519 · protein

SK678 binding region (siglec + unique)

6EFI · Kxykxgkxw signal domain protein: “SK678 binding region (siglec + unique)”. X-ray diffraction, 2 ligands (CA, CO), 2 pockets (best druggability 0.70). MolNFT v1 #147519 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6EFI
Type: protein
Length: 413 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Kxykxgkxw signal domain protein
UniProt: F0FS71
Ligands: CA, CO
Pockets: 2 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 12% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Kxykxgkxw signal domain protein	protein	205	12% helix, 38% strand	F0FS71
B	Kxykxgkxw signal domain protein	protein	208	12% helix, 35% strand	F0FS71

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B
CO · Cobalt (II) ion · metal · chains A
EDO · 1,2-ethanediol · additive · 13 copies · chains A, B
GOL · Glycerol · additive · 8 copies · chains A, B

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

Pockets

2 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	929	0.70	0.75	54	EDO
2	117	0.53	0.82	25	empty

Interfaces

1 interface between chains.

A–B · 445 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

6EFI · SK678 binding region (Siglec + Unique) · 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 F0FS71
Elsewhere: RCSB PDB 6EFI · PDBe 6EFI · UniProt F0FS71

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