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Crystal structure of unliganded HIV-1 clade C strain C1086 GP120 core

Analyse Crystal structure of unliganded HIV-1 clade C strain C1086 GP120 core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3TGR
Type: protein
Length: 692 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 clade C1086 GP120
Ligands: NAG
Pockets: 9 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	HIV-1 clade C1086 GP120	protein	346	15% helix, 35% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B

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

Pockets

9 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	587	0.73	0.81	68	NAG
2	110	0.63	0.88	26	empty
3	77	0.58	0.88	20	empty
4	161	0.56	0.81	23	NAG
5	80	0.43	0.80	19	empty

Interfaces

1 interface between chains.

A–B · 400 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 14 disulfide, 14 glycan (disulfide, N-glycosylation).

Compared structures

3TGR · Crystal structure of unliganded HIV-1 clade C strain C1086 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 3TGR · PDBe 3TGR

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