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HIV neutralizing monoclonal antibody YZ18

Analyse HIV neutralizing monoclonal antibody YZ18 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3CMO
Type: protein
Length: 863 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 0.64

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 51% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	Fab light chain	protein	210	6% helix, 50% strand	—
H, Y	Fab heavy chain	protein	222	9% helix, 52% strand	—
X	Fab light chain	protein	209	6% helix, 51% strand	—

Pockets

10 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	510	0.64	0.77	49	empty
2	368	0.56	0.74	58	empty
3	316	0.54	0.75	55	empty
4	164	0.47	0.77	29	empty
5	102	0.43	0.78	23	empty

Interfaces

5 interfaces between chains.

L–H · 1891 Å² buried · 22 hydrogen bonds · protein-protein
X–Y · 1851 Å² buried · 21 hydrogen bonds · protein-protein
L–Y · 290 Å² buried · 4 hydrogen bonds · protein-protein
H–X · 285 Å² buried · 1 hydrogen bond · protein-protein
L–X · 276 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3CMO · HIV neutralizing monoclonal antibody YZ18 · the same entry in another collection · chain H against H, 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 3CMO · PDBe 3CMO

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