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Crystal structure of unliganded HIV-1 clade A/E strain 93TH057 GP120 core

Analyse Crystal structure of unliganded HIV-1 clade A/E strain 93TH057 GP120 core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3TGT
Type: protein
Length: 342 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 clade A/E 93TH057 GP120
Ligands: NAG
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	HIV-1 clade A/E 93TH057 GP120	protein	342	20% helix, 37% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A
EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	60	0.55	0.88	18	NAG
2	66	0.37	0.79	20	empty
3	52	0.36	0.80	17	empty

Modifications

Observed in the structure: 10 glycan, 8 disulfide (N-glycosylation, disulfide).

Compared structures

3TGT · Crystal structure of unliganded HIV-1 clade A/E strain 93TH057 gp120 core · the same entry in another collection · chain A against A, 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 3TGT · PDBe 3TGT

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