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PIE12 D-peptide against HIV entry

Analyse PIE12 D-peptide against HIV entry in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3L35
Type: protein
Length: 182 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GP41 N-peptide; HIV entry inhibitor PIE12
Ligands: ACE, NH2

Structure

x-ray diffraction · 3 distinct chains · 84% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	GP41 N-peptide	protein	45	96% helix, 0% strand	—
H, K	HIV entry inhibitor PIE12	protein	16	63% helix, 0% strand	—
L	HIV entry inhibitor PIE12	protein	15	73% helix, 0% strand	—

Ligands and binding sites

ACE · Acetyl group · ligand · 5 copies · chains A, B, C, H, K
NH2 · Amino group · ion · 6 copies · chains A, B, C, H, K, L

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

Interfaces

9 interfaces between chains.

A–B · 980 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 960 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 960 Å² buried · 4 hydrogen bonds · protein-protein
A–H · 401 Å² buried · 3 hydrogen bonds · protein-protein
B–K · 379 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 44 d-amino, 5 covalent, 3 disulfide (D-amino acid, covalent ligand, disulfide).

Compared structures

3L35 · PIE12 D-peptide against HIV entry · 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 3L35 · PDBe 3L35

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