SMTL ID : 7ekk.1

Anti-HIV-1 broadly neutralizing antibody delta-loop 4E10 modified with pyrene acetamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: G.65, I.67, T.68 Ligands: NH4.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.67 Water bridges: A:Q.64, A:G.65, A:G.65

1 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.2: 1 residues within 4Å: Ligands: SO4.1 No protein-ligand interaction detected (PLIP)

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 4 residues within 4Å: Chain A: S.131, V.132, V.218, K.220 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.132, A:V.132, A:K.220 GOL.4: 7 residues within 4Å: Chain A: R.37, Q.38, A.39, R.42, G.43, E.45, R.62 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.37, A:A.39, A:G.43, A:E.45, A:R.62 GOL.6: 5 residues within 4Å: Chain B: Q.11, L.13, R.18, A.19, T.20 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.11, B:Q.11, B:T.20 GOL.7: 11 residues within 4Å: Chain A: F.177, P.178, V.180, S.188, L.189, S.190 Chain B: Q.161, S.163, S.177, S.178, T.179 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:F.177, A:S.188, A:S.190, B:S.163, B:S.178, B:T.179

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 4 residues within 4Å: Chain B: R.46, V.59, A.60, F.63 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rujas, E. et al., Focal accumulation of aromaticity at the CDRH3 loop mitigates 4E10 polyreactivity without altering its HIV neutralization profile. Iscience (2021)

Release Date

2021-08-11

Peptides

Heavy chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide: A
Light chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide: B
MPER region of the envelope glycoprotein gp41 from HIV-1: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
P

Heavy chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide

Light chain of the Fab region of Delta-loop variant of anti-HIV-1 broadly neutralizing antibody 4E10 modified with pyrene acetamide

MPER region of the envelope glycoprotein gp41 from HIV-1

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