SMTL ID : 7sx7.1 (1 other biounit)

Crystal structure of broadly neutralizing antibody N49P9.3-FR3-3 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: E.46, N.47 No protein-ligand interaction detected (PLIP) NAG.2: 7 residues within 4Å: Chain A: N.120, T.122, I.158, S.160, L.163, H.222 Ligands: EPE.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.163 Hydrogen bonds: A:N.120 Water bridges: A:S.160 NAG.3: 2 residues within 4Å: Chain A: N.115, N.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.115, A:N.127 Water bridges: A:K.117 NAG.4: 9 residues within 4Å: Chain A: D.97, P.98, K.138, N.148, N.246, C.308, V.309, S.310 Ligands: NAG.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.138, A:N.148, A:S.310 NAG.5: 6 residues within 4Å: Chain A: E.161, N.162 Chain C: H.24, I.25, I.26, Y.85 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:H.24, C:I.26, C:Y.85, A:N.162 Hydrophobic interactions: A:E.161 Water bridges: A:T.164 NAG.6: 6 residues within 4Å: Chain A: E.154, E.155, I.156, N.175, K.176, K.218 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.176 Hydrogen bonds: A:E.155, A:I.156, A:N.175, A:K.218, A:K.218 NAG.7: 2 residues within 4Å: Chain A: N.181, E.202 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.181, A:E.202, A:E.202 Water bridges: A:T.183 NAG.8: 3 residues within 4Å: Chain A: N.204, T.206, K.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.204, A:K.207 NAG.9: 2 residues within 4Å: Chain A: N.255, T.257 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.257 Water bridges: A:Q.258 NAG.10: 5 residues within 4Å: Chain A: N.261, T.263, C.264, G.272, C.273 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.261, A:G.272 Water bridges: A:N.261, A:N.261 NAG.11: 3 residues within 4Å: Chain A: S.177, N.311 Ligands: NAG.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.177, A:S.177, A:N.311

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.12: 6 residues within 4Å: Chain A: N.118, F.119, N.120, P.124, K.126 Ligands: NAG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.120, A:N.120 Salt bridges: A:K.126

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tolbert, W.D. et al., Crystal structure of broadly neutralizing antibody N49P9.3-FR3-3 Fab in complex with HIV-1 Clade A/E strain 93TH057 gp120 core. To Be Published

Release Date

2022-11-30

Peptides

clade A/E 93TH057 HIV-1 gp120 core: A
N49P9.3-FR3-3 ANTIBODY FAB HEAVY CHAIN: B
N49P9.3-FR3-3 ANTIBODY 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

N49P9.3-FR3-3 ANTIBODY FAB HEAVY CHAIN

N49P9.3-FR3-3 ANTIBODY FAB LIGHT CHAIN

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