Research workbench

DIABODY

Analyse DIABODY in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5FCS
Type: protein
Length: 473 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Diabody
Ligands: SO4
Pockets: 5 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Diabody	protein	233	6% helix, 50% strand	—
L	Diabody	protein	240	8% helix, 50% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains L

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	680	0.84	0.88	63	SO4
2	183	0.54	0.79	26	empty
3	219	0.53	0.77	44	empty
4	154	0.42	0.74	25	empty
5	112	0.38	0.74	19	empty

Interfaces

1 interface between chains.

H–L · 2189 Å² buried · 20 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 disulfide (disulfide).

Compared structures

5FCS · Diabody · 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 5FCS · PDBe 5FCS

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