MolNFT v1 · #173595 · protein

Broadly neutralizing darpin BND.1 in complex with the HIV-1 envelope variable loop 3 crown mimetic peptide V3-if (BG505)

7B4T: “Broadly neutralizing darpin BND.1 in complex with the HIV-1 envelope variable loop 3 crown mimetic peptide…”. X-ray diffraction, 1 ligand (SO4). MolNFT v1 #173595 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7B4T
Type: protein
Length: 177 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: HIV-1 envelope variable loop 3 crown mimetic peptide V3-if (BG505); Broadly neutralizing…
Ligands: SO4

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	HIV-1 envelope variable loop 3 crown mimetic peptide V3-if (BG505)	protein	15	0% helix, 13% strand	—
A	Broadly neutralizing darpin BND.1	protein	162	55% helix, 0% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A

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

Interfaces

1 interface between chains.

B–A · 714 Å² buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 d-amino (D-amino acid).

Compared structures

7B4T · Broadly neutralizing DARPin bnD.1 in complex with the HIV-1 envelope variable loop 3… · the same entry in another collection · chain B against B, 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 7B4T · PDBe 7B4T

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