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Crystal structure of broadly neutralizing anti-HIV-1 antibody CH103

Analyse Crystal structure of broadly neutralizing anti-HIV-1 antibody CH103 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4JAM
Type: protein
Length: 853 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Antigen binding fragment of heavy chain of CH103; Antigen binding fragment of light chain…
Ligands: SO4
Pockets: 7 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 7% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Antigen binding fragment of heavy chain of CH103	protein	223	5% helix, 51% strand	—
L	Antigen binding fragment of light chain of CH103	protein	206	7% helix, 52% strand	—
A	Antigen binding fragment of heavy chain of CH103	protein	219	8% helix, 51% strand	—
B	Antigen binding fragment of light chain of CH103	protein	205	7% helix, 53% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 16 copies · chains H, L, B, A
EDO · 1,2-ethanediol · additive · 12 copies · chains H, L, A, B
GOL · Glycerol · additive · chains H, L

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

Pockets

7 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	866	0.74	0.78	78	SO4
2	618	0.70	0.78	72	EDO, SO4
3	571	0.69	0.78	61	EDO
4	717	0.66	0.75	61	SO4
5	87	0.41	0.78	17	empty

Interfaces

5 interfaces between chains.

H–L · 1881 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 1878 Å² buried · 10 hydrogen bonds · protein-protein
L–A · 244 Å² buried · 1 hydrogen bond · protein-protein
H–B · 239 Å² buried · 3 hydrogen bonds · protein-protein
L–B · 200 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

4JAM · Crystal structure of broadly neutralizing anti-hiv-1 antibody ch103 · 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 4JAM · PDBe 4JAM

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