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HIV-1 GP120 envelope glycoprotein complexed with the broadly neutralizing CD4-binding-site antibody B12

Analyse HIV-1 GP120 envelope glycoprotein complexed with the broadly neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2NY7
Type: protein
Length: 735 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein GP120; Antibody B12, heavy chain; Antibody B12, light chain
UniProt: P04578
Ligands: NAG
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 46% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	Envelope glycoprotein GP120	protein	290	11% helix, 40% strand	P04578
H	Antibody B12, heavy chain	protein	230	8% helix, 48% strand	—
L	Antibody B12, light chain	protein	215	6% helix, 51% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains G, H

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	901	0.75	0.78	101	empty
2	58	0.60	0.92	22	empty
3	314	0.53	0.74	46	empty
4	93	0.42	0.78	21	empty
5	93	0.34	0.74	19	empty

Interfaces

2 interfaces between chains.

H–L · 2076 Å² buried · 12 hydrogen bonds · protein-protein
G–H · 1013 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

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

Compared structures

2NY7 · HIV-1 gp120 Envelope Glycoprotein Complexed with the Broadly Neutralizing… · 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 P04578
Elsewhere: RCSB PDB 2NY7 · PDBe 2NY7 · UniProt P04578

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