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Crystal structure of a glycosylase specific nanobody

Analyse Crystal structure of a glycosylase specific nanobody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8FTT
Type: protein
Length: 501 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.08
Source: synthetic construct
Molecule: Anti-NEIL1 Nanobody
Ligands: SO4
Pockets: 2 · best druggability 0.65

Structure

x-ray diffraction · resolution 2.08 · 3 distinct chains · 2% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Anti-NEIL1 Nanobody	protein	128	2% helix, 49% strand	—
C	Anti-NEIL1 Nanobody	protein	120	3% helix, 56% strand	—
D	Anti-NEIL1 Nanobody	protein	125	2% helix, 49% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B, D

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

Pockets

2 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	574	0.65	0.76	52	empty
2	255	0.60	0.80	47	empty

Interfaces

4 interfaces between chains.

A–C · 1026 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 878 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 256 Å² buried · 1 hydrogen bond · protein-protein
B–C · 156 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 8FTT · PDBe 8FTT

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