MolNFT v1 · #60225 · protein

HIV neutralizing monoclonal antibody YZ23

3CLF · Fab light chain: “HIV neutralizing monoclonal antibody YZ23”. X-ray diffraction, 6 pockets (best druggability 0.63). MolNFT v1 #60225 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3CLF
Type: protein
Length: 434 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab light chain; Fab heavy chain
Pockets: 6 · best druggability 0.63

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab light chain	protein	214	6% helix, 51% strand	—
H	Fab heavy chain	protein	220	8% helix, 54% strand	—

Pockets

6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	176	0.63	0.84	27	empty
2	424	0.56	0.73	56	empty
3	68	0.54	0.87	23	empty
4	96	0.38	0.76	18	empty
5	77	0.35	0.76	17	empty

Interfaces

1 interface between chains.

L–H · 1925 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

3CLF · HIV neutralizing monoclonal antibody YZ23 · 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 3CLF · PDBe 3CLF

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