MolNFT v1 · #176687 · protein

Crystal structure of Fab fragment of daratumumab

7DUN · Fab heavy chain: “Crystal structure of Fab fragment of daratumumab”. X-ray diffraction, 5 pockets (best druggability 0.61). MolNFT v1 #176687 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7DUN
Type: protein
Length: 432 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab heavy chain; Fab light chain
Pockets: 5 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab heavy chain	protein	220	9% helix, 51% strand	—
L	Fab light chain	protein	212	6% helix, 51% strand	—

Pockets

5 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	593	0.61	0.73	57	empty
2	92	0.40	0.77	20	empty
3	60	0.31	0.76	17	empty
4	67	0.29	0.73	15	empty
5	50	0.28	0.75	15	empty

Interfaces

1 interface between chains.

H–L · 1889 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7DUN · Crystal structure of Fab fragment of Daratumumab · 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 7DUN · PDBe 7DUN

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