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Crystal structure of a polysaccharide-binding human Fab (F598) in complex with nona-N-acetyl-D-glucosamine (9NAC)

Analyse Crystal structure of a polysaccharide-binding human Fab (F598) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6BE4
Type: protein
Length: 430 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab (F598) heavy chain; FAB(F598) light chain
Ligands: NAG
Pockets: 2 · best druggability 0.55

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab (F598) heavy chain	protein	217	9% helix, 53% strand	—
L	FAB(F598) light chain	protein	213	8% helix, 54% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	424	0.55	0.73	48	empty
2	51	0.38	0.81	16	empty

Interfaces

1 interface between chains.

H–L · 1577 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6BE4 · Crystal structure of a polysaccharide-binding human Fab (F598) in complex with… · 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 6BE4 · PDBe 6BE4

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