MolNFT v1 · #171192 · protein

De novo designed protein 4H_01 in complex with mota antibody

6YWD · Antibody mota, heavy chain: “De novo designed protein 4H_01 in complex with mota antibody”. X-ray diffraction, 4 pockets (best druggability 0.62). MolNFT v1 #171192 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YWD
Type: protein
Length: 511 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antibody mota, heavy chain; Antibody mota, light chain; De novo designed protein 4H_01
Pockets: 4 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 16% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Antibody mota, heavy chain	protein	223	5% helix, 51% strand	—
B	Antibody mota, light chain	protein	213	6% helix, 51% strand	—
C	De novo designed protein 4H_01	protein	75	76% helix, 0% strand	—

Pockets

4 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	602	0.62	0.74	60	empty
2	102	0.50	0.81	28	empty
3	67	0.46	0.84	22	empty
4	54	0.27	0.74	17	empty

Interfaces

3 interfaces between chains.

A–B · 2005 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 510 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 236 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide (disulfide).

Compared structures

6YWD · De novo designed protein 4H_01 in complex with Mota antibody · the same entry in another collection · chain A against A, 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 6YWD · PDBe 6YWD

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