SMTL ID : 8aed.2 (1 other biounit)

Broadly neutralizing DARPin bnD.9 in complex with the HIV-1 envelope variable loop 3 peptide V3 (BG505)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.17 Å

Oligo State

hetero-1-1-mer

Ligands

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 4 residues within 4Å: Chain A: F.99, D.128, A.131, Q.132 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.128, A:Q.132, A:Q.132 EDO.2: 7 residues within 4Å: Chain A: Y.13, Y.46, F.47 Chain B: K.4, G.18, I.21, G.22 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.46, B:K.4 Water bridges: A:Y.46

1 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 2 residues within 4Å: Chain A: E.117 Ligands: CIT.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.117, H2O.4

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.4: 8 residues within 4Å: Chain A: G.81, L.83, G.114, H.115, L.116, E.117, I.118 Ligands: MG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.117, A:I.118 Water bridges: A:L.83 Salt bridges: A:H.115

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Glogl, M. et al., Trapping the HIV-1 V3 loop in a helical conformation enables broad neutralization. Nat.Struct.Mol.Biol. (2023)

Release Date

2023-08-16

Peptides

Broadly neutralizing DARPin bnD.9: A
Envelope glycoprotein gp160: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

Broadly neutralizing DARPin bnD.9

Envelope glycoprotein gp160

Related Entries With Identical Sequence