MolNFT v1 · #100939 · protein

Neutralizing antibody to murine norovirus

4NCC · Fab fragment light: “Neutralizing antibody to murine norovirus”. X-ray diffraction, 14 pockets (best druggability 0.54). MolNFT v1 #100939 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4NCC
Type: protein
Length: 861 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab fragment light; Fab fragment heavy
Pockets: 14 · best druggability 0.54

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab fragment light	protein	211	5% helix, 54% strand	—
H, 2	Fab fragment heavy	protein	220	4% helix, 50% strand	—
1	Fab fragment light	protein	210	5% helix, 54% strand	—

Pockets

14 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	334	0.54	0.74	39	empty
2	312	0.53	0.74	43	empty
3	69	0.48	0.84	22	empty
4	176	0.46	0.75	26	empty
5	156	0.46	0.76	25	empty

Interfaces

4 interfaces between chains.

L–H · 1810 Å² buried · 20 hydrogen bonds · protein-protein
1–2 · 1761 Å² buried · 16 hydrogen bonds · protein-protein
H–1 · 342 Å² buried · 8 hydrogen bonds · protein-protein
L–1 · 125 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4NCC · Neutralizing antibody to murine norovirus · the same entry in another collection · chain L against L, 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
Elsewhere: RCSB PDB 4NCC · PDBe 4NCC

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