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Fusion surface structure, function, and dynamics of gamete fusogen HAP2

Analyse Fusion surface structure, function, and dynamics of gamete fusogen HAP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6DBS
Type: protein
Length: 1,546 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hapless 2
UniProt: A4GRC6
Ligands: NAG, BMA, MAN
Pockets: 20 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hapless 2	protein	516	10% helix, 40% strand	A4GRC6
C, B	Hapless 2	protein	515	10% helix, 40% strand	A4GRC6

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, C, B
BMA · beta-D-mannopyranose · sugar · 3 copies
MAN · alpha-D-mannopyranose · sugar · 2 copies

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

Pockets

20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	442	0.86	0.94	60	empty
2	557	0.86	0.92	65	empty
3	497	0.86	0.92	67	empty
4	430	0.86	0.93	61	empty
5	379	0.76	0.87	48	empty

Interfaces

3 interfaces between chains.

A–B · 3548 Å² buried · 37 hydrogen bonds · protein-protein
A–C · 3525 Å² buried · 37 hydrogen bonds · protein-protein
C–B · 3522 Å² buried · 39 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 33 disulfide, 12 glycan (disulfide, N-glycosylation).

Compared structures

6DBS · Fusion surface structure, function, and dynamics of gamete fusogen HAP2 · the same entry in another collection · chain A against A, TM-score 1.00
A4GRC6 · AlphaFold monomer V2.0 prediction for hapless 2 (A4GRC6) · a predicted model of the same protein · chain C 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 A4GRC6
Elsewhere: RCSB PDB 6DBS · PDBe 6DBS · UniProt A4GRC6

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