MolNFT v1 · #96922 · protein

Crystal structure of human Fab PGT122, a broadly reactive and potent HIV-1 neutralizing antibody

4JY5 · PGT122 light chain: “Crystal structure of human Fab PGT122, a broadly reactive and potent HIV-1 neutralizing antibody”. X-ray diffraction, 3 pockets (best druggability 0.67). MolNFT v1 #96922 on GenesisL1: 3D structure, binding…

PDB: 4JY5
Type: protein
Length: 426 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: PGT122 light chain; PGT122 heavy chain
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 2 distinct chains · 8% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	PGT122 light chain	protein	200	7% helix, 47% strand	—
H	PGT122 heavy chain	protein	226	9% helix, 52% strand	—

Ligands and binding sites

GOL · Glycerol · additive · 3 copies · chains L, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 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	698	0.67	0.76	61	GOL
2	69	0.33	0.76	18	GOL
3	83	0.32	0.74	17	empty

Interfaces

1 interface between chains.

L–H · 1937 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

4JY5 · Crystal structure of human Fab PGT122, a broadly reactive and potent HIV-1 neutralizing… · 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 4JY5 · PDBe 4JY5

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