Research workbench

Crystal structure of the inner domain of clade A/E HIV-1 GP120 in complex with the adcc-potent rhesus macaque antibody JR4

Analyse Crystal structure of the inner domain of clade A/E HIV-1 GP120 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5FCU
Type: protein
Length: 533 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Clade A/E 93TH057 HIV-1 GP120 core; JR4 Fab heavy chain; JR4 Fab light chain
UniProt: A0A0M3KKW9
Ligands: NAG, SO4, CL
Pockets: 6 · best druggability 0.69

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Clade A/E 93TH057 HIV-1 GP120 core	protein	104	12% helix, 34% strand	A0A0M3KKW9
H	JR4 Fab heavy chain	protein	217	9% helix, 52% strand	—
L	JR4 Fab light chain	protein	212	6% helix, 52% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains G
SO4 · Sulfate ion · ion · 3 copies · chains L, H
CL · Chloride ion · ion · 3 copies · chains L

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	755	0.69	0.76	78	SO4
2	302	0.60	0.78	50	empty
3	161	0.44	0.75	25	empty
4	100	0.40	0.76	29	empty
5	53	0.34	0.78	12	empty

Interfaces

3 interfaces between chains.

H–L · 1753 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 856 Å² buried · 17 hydrogen bonds · protein-protein
G–L · 174 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

5FCU · Crystal structure of the inner domain of clade A/E HIV-1 GP120 in complex with the… · 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
Every structure of UniProt A0A0M3KKW9
Elsewhere: RCSB PDB 5FCU · PDBe 5FCU · UniProt A0A0M3KKW9

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.