MolNFT v1 · #161788 · protein

Drosophila semaphorin 2A

6QP7 · Semaphorin-2A: “Drosophila semaphorin 2A”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 17 pockets (best druggability 0.81). MolNFT v1 #161788 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6QP7
Type: protein
Length: 1,239 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Semaphorin-2A
UniProt: Q24323
Ligands: NAG, MAN, BMA, CL
Pockets: 17 · best druggability 0.81

Structure

x-ray diffraction · 2 distinct chains · 11% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Semaphorin-2A	protein	620	10% helix, 43% strand	Q24323
B	Semaphorin-2A	protein	619	11% helix, 43% strand	Q24323

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B
MAN · alpha-D-mannopyranose · sugar · 15 copies · chains A, B
BMA · beta-D-mannopyranose · sugar · 5 copies · chains A, B
CL · Chloride ion · ion · 4 copies · chains A, B
EDO · 1,2-ethanediol · additive · 18 copies · chains A, B

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

Pockets

17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	610	0.81	0.86	60	EDO
2	788	0.78	0.82	50	empty
3	835	0.77	0.80	60	NAG
4	185	0.60	0.82	35	empty
5	173	0.59	0.82	33	empty

Interfaces

1 interface between chains.

A–B · 2059 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 21 disulfide, 11 glycan (disulfide, N-glycosylation).

Compared structures

6QP7 · Drosophila Semaphorin 2a · the same entry in another collection · chain A against A, TM-score 1.00
Q24323 · AlphaFold monomer V2.0 prediction for semaphorin-2A (Q24323) · a predicted model of the same protein · 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 Q24323
Elsewhere: RCSB PDB 6QP7 · PDBe 6QP7 · UniProt Q24323

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