Research workbench

GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-27

Analyse GII.10 Vietnam 026 protruding domain in complex with Nanobody Nano-27 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OMN
Type: protein
Length: 425 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.682
Source: Norwalk virus; Vicugna pacos
Molecule: Capsid protein; Nanobody (VHH) Nano-27
UniProt: Q5F4T5
Pockets: 3 · best druggability 0.40

Structure

x-ray diffraction · resolution 2.682 · 2 distinct chains · 5% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Capsid protein	protein	312	6% helix, 35% strand	Q5F4T5
C	Nanobody (VHH) Nano-27	protein	113	3% helix, 51% strand	—

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	89	0.40	0.77	22	empty
2	86	0.35	0.74	16	empty
3	69	0.28	0.73	17	empty

Interfaces

1 interface between chains.

B–C · 570 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

5OMN · GII.10 vietnam 026 protruding domain in complex with nanobody nano-27 · the same entry in another collection · chain B against B, 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 Q5F4T5
Elsewhere: RCSB PDB 5OMN · PDBe 5OMN · UniProt Q5F4T5

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