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HIV-1 V3 loop mimic

Analyse HIV-1 V3 loop mimic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1AI1
Type: protein
Length: 446 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: IGG1-kappa 59.1 Fab (light chain); IGG1-kappa 59.1 Fab (heavy chain); AIB142
UniProt: P01868, P05877
Pockets: 4 · best druggability 0.58

Structure

x-ray diffraction · 3 distinct chains · 5% helix, 52% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
L	IGG1-kappa 59.1 Fab (light chain)	protein	215	6% helix, 54% strand	—
H	IGG1-kappa 59.1 Fab (heavy chain)	protein	221	5% helix, 52% strand	P01868
P	AIB142	protein	10	0% helix, 0% strand	P05877

Pockets

4 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	456	0.58	0.74	54	empty
2	108	0.43	0.78	18	empty
3	55	0.30	0.76	14	empty
4	60	0.28	0.74	14	empty

Interfaces

3 interfaces between chains.

L–H · 1780 Å² buried · 17 hydrogen bonds · protein-protein
H–P · 326 Å² buried · 3 hydrogen bonds · protein-protein
L–P · 277 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 modified (disulfide, nonstandard).

Compared structures

1AI1 · HIV-1 V3 loop mimic · the same entry in another collection · chain L against L, TM-score 1.00
P01868 · AlphaFold monomer V2.0 prediction for ig gamma-1 chain C region secreted form (P01868) · a predicted model of the same protein · chain H against A, TM-score 0.51

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 P01868
Every structure of UniProt P05877
Elsewhere: RCSB PDB 1AI1 · PDBe 1AI1 · UniProt P01868 · UniProt P05877

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