SMTL ID : 6bck.1

Crystal Structure of Broadly Neutralizing Antibody N49P7 in Complex with HIV-1 Clade AE strain 93TH057 gp120 core.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-1-1-1-mer

Ligands

11 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.1: 5 residues within 4Å: Chain A: N.118, G.121, P.122, S.158, L.161 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.161 Hydrogen bonds: A:N.118, A:G.121 NAG.2: 2 residues within 4Å: Chain A: N.113, N.125 No protein-ligand interaction detected (PLIP) NAG.3: 9 residues within 4Å: Chain A: D.95, P.96, K.136, V.138, N.146, R.246, C.306, V.307, S.308 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.138 Hydrogen bonds: A:K.136, A:N.146, A:R.246, A:S.308 NAG.4: 7 residues within 4Å: Chain A: E.159, N.160, T.162 Chain B: S.110 Chain C: N.27, L.28, Y.87 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 interactions with chain C Hydrogen bonds: B:S.110, A:N.160, C:N.27, C:Y.87 NAG.5: 5 residues within 4Å: Chain A: E.153, I.154, N.173, K.174, K.216 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.154, A:N.173, A:K.216 NAG.6: 4 residues within 4Å: Chain A: N.179, T.181, E.200, K.303 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.179, A:T.181, A:E.200, A:K.303 NAG.7: 2 residues within 4Å: Chain A: N.202, T.204 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain A: P.230, M.240, N.253, T.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.253 NAG.9: 5 residues within 4Å: Chain A: Q.256, N.259, T.261, C.262, C.271 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.256 Hydrogen bonds: A:T.261, A:C.271 NAG.10: 4 residues within 4Å: Chain A: N.146, G.147, S.175, N.309 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.175 NAG.11: 1 residues within 4Å: Chain A: N.223 No protein-ligand interaction detected (PLIP)

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

MPD.12: 4 residues within 4Å: Chain A: K.280, K.282, Q.283, I.284 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.283 MPD.13: 5 residues within 4Å: Chain A: G.320, A.321 Chain B: E.45, W.46 Chain C: E.88 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:E.88, B:E.45, B:W.46 Hydrogen bonds: C:E.88, B:W.46

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
N49P7 Fab heavy chain of N29P7 IgG: B
N49P7 Fab light chain from N49P7 IgG: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
H

C
L

clade A/E 93TH057 HIV-1 gp120 core

N49P7 Fab heavy chain of N29P7 IgG

N49P7 Fab light chain from N49P7 IgG

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