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Drosophila semaphorin 1B, extracellular domains 1-2

Analyse Drosophila semaphorin 1B, extracellular domains 1-2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6FKK
Type: protein
Length: 513 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: MIP07328P
UniProt: Q7KK54
Ligands: MAN, NAG, BMA
Pockets: 5 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 10% helix, 41% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	MIP07328P	protein	513	10% helix, 41% strand	Q7KK54

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
BMA · beta-D-mannopyranose · sugar · 2 copies

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

Pockets

5 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	686	0.72	0.79	61	empty
2	125	0.62	0.87	23	empty
3	160	0.50	0.77	18	empty
4	121	0.48	0.79	18	empty
5	130	0.44	0.77	19	empty

Modifications

Observed in the structure: 7 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

6FKK · Drosophila Semaphorin 1b, extracellular domains 1-2 · 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 Q7KK54
Elsewhere: RCSB PDB 6FKK · PDBe 6FKK · UniProt Q7KK54

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