MolNFT v1 · #146259 · protein

Apo Fab structure of mouse monoclonal antibody 8B2

6DC7 · Fab light chain: “Apo Fab structure of mouse monoclonal antibody 8B2”. X-ray diffraction, 10 pockets (best druggability 0.65). MolNFT v1 #146259 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6DC7
Type: protein
Length: 857 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain
Pockets: 10 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L, M	Fab light chain	protein	218	6% helix, 53% strand	—
H	Fab heavy chain	protein	210	9% helix, 55% strand	—
I	Fab heavy chain	protein	211	9% helix, 55% strand	—

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	662	0.65	0.75	61	empty
2	128	0.61	0.85	19	empty
3	174	0.60	0.82	23	empty
4	471	0.57	0.73	52	empty
5	192	0.43	0.73	29	empty

Interfaces

3 interfaces between chains.

M–I · 1685 Å² buried · 7 hydrogen bonds · protein-protein
L–H · 1661 Å² buried · 6 hydrogen bonds · protein-protein
L–M · 648 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

6DC7 · Apo Fab structure of mouse monoclonal antibody 8B2 · 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 6DC7 · PDBe 6DC7

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