SMTL ID : 5wb9.1

Crystal structure of CD4 binding site antibody N60P23 in complex with HIV-1 clade A/E strain 93TH057 gp120 core

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-1-mer

Ligands

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 5 residues within 4Å: Chain A: N.118, T.120, I.156, L.161, H.220 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118, A:T.120, A:T.120 NAG.2: 2 residues within 4Å: Chain A: N.113, N.125 No protein-ligand interaction detected (PLIP) NAG.3: 7 residues within 4Å: Chain A: P.96, K.136, N.146, N.244, C.306, V.307, S.308 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.136, A:S.308 NAG.4: 5 residues within 4Å: Chain A: E.152, E.153, I.154, N.173, K.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.153, A:I.154 Water bridges: A:N.173 NAG.5: 5 residues within 4Å: Chain A: E.177, N.179, T.181, Y.198, E.200 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.179, A:Y.198, A:E.200, A:K.303 NAG.6: 3 residues within 4Å: Chain A: M.240, N.253, T.255 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.255 Water bridges: A:N.253, A:T.255 NAG.7: 5 residues within 4Å: Chain A: Q.256, N.259, C.262, K.269, C.271 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.256 Hydrogen bonds: A:K.269 NAG.8: 4 residues within 4Å: Chain A: N.146, G.147, S.175, N.309 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.175 Water bridges: A:S.175

1 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.9: 9 residues within 4Å: Chain A: W.69, V.139, T.141, E.237, S.242, F.243, W.288, G.334, I.336 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.69, A:V.139, A:T.141, A:I.336

1 x MPO: 3[N-MORPHOLINO]PROPANE SULFONIC ACID(Non-covalent)

MPO.10: 5 residues within 4Å: Chain A: R.195, I.281, K.282, Q.283, I.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.282, A:Q.283

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sajadi, M.M. et al., Identification of Near-Pan-neutralizing Antibodies against HIV-1 by Deconvolution of Plasma Humoral Responses. Cell (2018)

Release Date

2018-05-23

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
N60P23 Fab heavy chain: B
N60P23 Fab light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

clade A/E 93TH057 HIV-1 gp120 core

N60P23 Fab heavy chain

N60P23 Fab light chain

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