MolNFT v1 · #182663 · protein

Crystal structure of the apo F240 antibody fragment

7N04 · Fab F240 heavy chain: “Crystal structure of the apo F240 antibody fragment”. X-ray diffraction, 1 ligand (GLC), 2 pockets (best druggability 0.50). MolNFT v1 #182663 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7N04
Type: protein
Length: 443 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab F240 heavy chain; Fab F240 light chain
Ligands: GLC
Pockets: 2 · best druggability 0.50

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 53% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab F240 heavy chain	protein	226	9% helix, 55% strand	—
L	Fab F240 light chain	protein	217	6% helix, 52% strand	—

Ligands and binding sites

GLC · alpha-D-glucopyranose · sugar · chains H, L

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

Pockets

2 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	206	0.50	0.76	32	empty
2	192	0.46	0.74	37	empty

Interfaces

1 interface between chains.

H–L · 1766 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7N04 · Crystal structure of the apo F240 antibody fragment · the same entry in another collection · chain H against H, 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 7N04 · PDBe 7N04

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