Research workbench

HIV-1 GP120 envelope GLYCOPROTEIN(S334A) complexed with CD4 and antibody 17B

Analyse HIV-1 GP120 envelope GLYCOPROTEIN(S334A) complexed with CD4 and antibody 17B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2NXY
Type: protein
Length: 926 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein GP120; T-cell surface glycoprotein CD4; Antibody 17B, light chain…
UniProt: Q49DS8, P01730, Q6P5S8, Q6N095
Ligands: NAG
Pockets: 11 · best druggability 0.70

Structure

x-ray diffraction · 4 distinct chains · 11% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Envelope glycoprotein GP120	protein	304	17% helix, 38% strand	Q49DS8
B	T-cell surface glycoprotein CD4	protein	181	8% helix, 51% strand	P01730
C	Antibody 17B, light chain	protein	214	6% helix, 50% strand	Q6P5S8
D	Antibody 17B, heavy chain	protein	227	8% helix, 51% strand	Q6N095

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A, B
HEZ · Hexane-1,6-diol · additive · 3 copies · chains A, C, D
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	51	0.70	0.98	17	TRS
2	53	0.69	0.98	19	empty
3	440	0.59	0.75	52	empty
4	317	0.57	0.77	40	empty
5	85	0.55	0.85	22	NAG

Interfaces

4 interfaces between chains.

C–D · 1825 Å² buried · 14 hydrogen bonds · protein-protein
A–B · 1148 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 539 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 144 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 13 disulfide, 13 glycan (disulfide, N-glycosylation).

Compared structures

2NXY · HIV-1 gp120 Envelope Glycoprotein(S334A) Complexed with CD4 and Antibody 17b · the same entry in another collection · chain A against A, TM-score 1.00
P01730 · AlphaFold monomer V2.0 prediction for T-cell surface glycoprotein CD4 (P01730) · a predicted model of the same protein · chain B against A, TM-score 0.97

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 Q49DS8
Every structure of UniProt P01730
Every structure of UniProt Q6P5S8
Every structure of UniProt Q6N095
Elsewhere: RCSB PDB 2NXY · PDBe 2NXY · UniProt Q49DS8 · UniProt P01730 · UniProt Q6P5S8 · UniProt Q6N095

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