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Antibody 64M-5 Fab in ligand-free form

Analyse Antibody 64M-5 Fab in ligand-free form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6IDH
Type: protein
Length: 434 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain); Anti-(6-4) photoproduct…
Pockets: 6 · best druggability 0.56

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Anti-(6-4) photoproduct antibody 64M-5 Fab (light chain)	protein	217	6% helix, 52% strand	—
H	Anti-(6-4) photoproduct antibody 64M-5 Fab (heavy chain)	protein	217	8% helix, 53% strand	—

Pockets

6 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	366	0.56	0.75	53	empty
2	103	0.39	0.76	20	empty
3	135	0.39	0.74	21	empty
4	58	0.31	0.75	15	empty
5	65	0.25	0.72	14	empty

Interfaces

1 interface between chains.

L–H · 1717 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6IDH · Antibody 64M-5 Fab in ligand-free form · 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 6IDH · PDBe 6IDH

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