MolNFT v1 · #96123 · protein

Crystal structure of broadly neutralizing antibody CH103 in complex with HIV-1 GP120

4JAN · Envelope glycoprotein GP120 of HIV-1 clade C: “Crystal structure of broadly neutralizing antibody CH103 in complex with HIV-1 GP120”. X-ray diffraction, 2 ligands (NAG, NA), 14 pockets (best druggability 0.74). MolNFT v1 #96123 on…

PDB: 4JAN
Type: protein
Length: 1,164 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein GP120 of HIV-1 clade C; Antigen binding fragment of heavy chain of…
Ligands: NAG, NA
Pockets: 14 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 9% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Envelope glycoprotein GP120 of HIV-1 clade C	protein	160	11% helix, 38% strand	—
H, A	Antigen binding fragment of heavy chain of CH103	protein	218	6% helix, 49% strand	—
L, B	Antigen binding fragment of light chain of CH103	protein	206	6% helix, 50% strand	—
I	Envelope glycoprotein GP120 of HIV-1 clade C	protein	156	16% helix, 40% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains G, I, H
NA · Sodium ion · metal · 2 copies · chains H, L, B
GOL · Glycerol · additive · 2 copies · chains L, B

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

Pockets

14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	934	0.74	0.78	73	NA, GOL
2	966	0.70	0.75	89	GOL
3	682	0.68	0.77	67	NAG
4	303	0.55	0.76	45	empty
5	176	0.48	0.76	23	empty

Interfaces

10 interfaces between chains.

H–L · 1815 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1756 Å² buried · 9 hydrogen bonds · protein-protein
H–B · 765 Å² buried · 4 hydrogen bonds · protein-protein
G–H · 505 Å² buried · 15 hydrogen bonds · protein-protein
I–A · 474 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 10 glycan (disulfide, N-glycosylation).

Compared structures

4JAN · crystal structure of broadly neutralizing antibody CH103 in complex with HIV-1 gp120 · the same entry in another collection · chain G against G, 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 4JAN · PDBe 4JAN

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