Research workbench

Mouse semaphorin 6A extracellular domain

Analyse Mouse semaphorin 6A extracellular domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3AFC
Type: protein
Length: 1,033 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Semaphorin-6A
UniProt: O35464
Ligands: NAG
Pockets: 11 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Semaphorin-6A	protein	534	10% helix, 38% strand	O35464
B	Semaphorin-6A	protein	499	9% helix, 39% strand	O35464

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	623	0.82	0.87	57	empty
2	912	0.79	0.81	61	empty
3	602	0.77	0.83	45	empty
4	172	0.49	0.77	30	empty
5	155	0.45	0.76	28	empty

Interfaces

1 interface between chains.

A–B · 1498 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

3AFC · Mouse Semaphorin 6A extracellular domain · the same entry in another collection · chain A against A, TM-score 1.00
O35464 · AlphaFold monomer V2.0 prediction for semaphorin-6A (O35464) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O35464
Elsewhere: RCSB PDB 3AFC · PDBe 3AFC · UniProt O35464

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