SMTL ID : 8aed.1 (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: G.48, H.49, L.50, E.51 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.50, A:E.51, A:E.51 EDO.2: 5 residues within 4Å: Chain A: N.68, R.69, E.101 Chain B: A.16, I.20 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.69 Water bridges: A:N.68, A:N.68, A:E.101

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 3 residues within 4Å: Chain A: V.63, N.64, G.93 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.64 Water bridges: A:V.63 ACT.4: 1 residues within 4Å: Chain A: K.157 4 PLIP interactions: 4 interactions with chain A Water bridges: A:K.157, A:K.157, A:K.157 Salt bridges: A:K.157

2 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 2 residues within 4Å: Chain A: E.117 Ligands: CIT.6 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.117, H2O.4 MG.7: 1 residues within 4Å: Chain B: D.23 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.23, H2O.10, H2O.10

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

CIT.6: 8 residues within 4Å: Chain A: G.81, L.83, G.114, H.115, L.116, E.117, I.118 Ligands: MG.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.116, 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
A

B
C

Broadly neutralizing DARPin bnD.9

Envelope glycoprotein gp160

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