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Crystal structure of the Fab fragment of kko

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

PDB: 4R97
Type: protein
Length: 432 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Platelet factor 4 antibody kko light chain; Platelet factor 4 antibody kko heavy chain
Ligands: ZN
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Platelet factor 4 antibody kko light chain	protein	214	7% helix, 50% strand	—
C	Platelet factor 4 antibody kko heavy chain	protein	218	9% helix, 52% strand	—

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains B, C
GOL · Glycerol · additive · 5 copies · chains B, C

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

Pockets

3 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	702	0.66	0.75	64	GOL
2	61	0.28	0.73	21	empty
3	59	0.25	0.72	17	empty

Interfaces

1 interface between chains.

B–C · 1864 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

4R97 · Crystal structure of the Fab fragment of KKO · 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
Elsewhere: RCSB PDB 4R97 · PDBe 4R97

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