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Crystal structure of sudan ebolavirus glycoprotein (strain gulu) bound to 16F6

Analyse Crystal structure of sudan ebolavirus glycoprotein (strain gulu) bound to 16F6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3S88
Type: protein
Length: 787 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 16F6 - heavy chain; Envelope glycoprotein; 16F6 - light chain
UniProt: Q7T9D9
Ligands: NAG
Pockets: 15 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	16F6 - heavy chain	protein	220	5% helix, 47% strand	—
I	Envelope glycoprotein	protein	249	9% helix, 32% strand	Q7T9D9
J	Envelope glycoprotein	protein	106	39% helix, 11% strand	Q7T9D9
L	16F6 - light chain	protein	212	5% helix, 49% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains I, J

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

Pockets

15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	333	0.69	0.82	47	empty
2	423	0.68	0.80	41	empty
3	303	0.61	0.79	47	empty
4	302	0.54	0.75	33	empty
5	206	0.52	0.77	26	empty

Interfaces

6 interfaces between chains.

I–J · 2436 Å² buried · 26 hydrogen bonds · protein-protein
H–L · 1773 Å² buried · 16 hydrogen bonds · protein-protein
H–I · 363 Å² buried · 6 hydrogen bonds · protein-protein
H–J · 265 Å² buried · 3 hydrogen bonds · protein-protein
J–L · 162 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

3S88 · Crystal structure of Sudan Ebolavirus Glycoprotein (strain Gulu) bound to 16F6 · the same entry in another collection · chain I against I, 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 Q7T9D9
Elsewhere: RCSB PDB 3S88 · PDBe 3S88 · UniProt Q7T9D9

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