MolNFT v1 · #102870 · protein

X-ray structure of the DC8E8 Fab apo-form crystallized at pH 8.5 and refined to 3.0 a.

4OZ4 · Fab of monoclonal antibody, heavy chain: “X-ray structure of the DC8E8 Fab apo-form crystallized at pH 8.5 and refined to 3.0 a.”. X-ray diffraction, 10 pockets (best druggability 0.72). MolNFT v1 #102870 on GenesisL1: 3D structure…

PDB: 4OZ4
Type: protein
Length: 876 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab of monoclonal antibody, heavy chain; Fab of monoclonal antibody, light chain
Pockets: 10 · best druggability 0.72

Structure

x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H, A	Fab of monoclonal antibody, heavy chain	protein	220	8% helix, 50% strand	—
L, B	Fab of monoclonal antibody, light chain	protein	218	5% helix, 54% strand	—

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1099	0.72	0.76	119	empty
2	752	0.67	0.75	65	empty
3	748	0.66	0.74	67	empty
4	192	0.54	0.79	28	empty
5	161	0.51	0.79	29	empty

Interfaces

5 interfaces between chains.

A–B · 1867 Å² buried · 19 hydrogen bonds · protein-protein
H–L · 1855 Å² buried · 19 hydrogen bonds · protein-protein
H–A · 278 Å² buried · 9 hydrogen bonds · protein-protein
H–B · 100 Å² buried · 0 hydrogen bonds · protein-protein
L–A · 70 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 4OZ4 · PDBe 4OZ4

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