SMTL ID : 8sww.1

BG505 Boost2 SOSIP.664 in complex with NHP polyclonal antibody IF3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

5 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.141, N.153, Y.170, L.172, D.325 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.170 NAG-NAG.2: 4 residues within 4Å: Chain A: N.390, S.392 Ligands: NAG.13, NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: N.300, T.302, H.334, N.336 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 10 residues within 4Å: Chain D: E.216, V.259, L.266, N.267, N.381, R.447, C.448, V.449, S.450 Ligands: NAG.20 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.449 NAG-NAG.7: 4 residues within 4Å: Chain F: N.300, T.302, H.334, N.336 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.4: 10 residues within 4Å: Chain A: E.216, V.259, L.266, N.267, F.380, N.381, G.383, V.449, S.450 Ligands: NAG.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.383, A:V.449

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.6: 8 residues within 4Å: Chain F: E.216, V.259, L.266, N.267, N.381, G.383, V.449, S.450 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:V.449

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

NAG.8: 5 residues within 4Å: Chain A: C.136, N.138, G.149, K.194, Y.196 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: Q.135, S.155, F.156, N.157 Ligand excluded by PLIP NAG.10: 4 residues within 4Å: Chain A: E.273, E.274, N.294, K.348 Ligand excluded by PLIP NAG.11: 6 residues within 4Å: Chain A: Q.298, N.300, N.336, V.337, S.338, R.447 Ligand excluded by PLIP NAG.12: 4 residues within 4Å: Chain A: N.267, S.296, N.451 Ligands: NAG-NAG-BMA.4 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain A: N.367, S.368, S.369 Ligands: NAG-NAG.2, NAG-NAG.2 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: S.392, N.396 Ligands: NAG-NAG.2 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: P.98, W.99, N.100, T.102 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain B: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain C: N.107, S.109, E.110 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain C: E.123, N.126 Ligand excluded by PLIP NAG.19: 5 residues within 4Å: Chain D: N.239, T.241, S.279, N.281, I.282 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain D: N.267, S.296, N.451 Ligands: NAG-NAG.5 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain D: N.300, T.302, H.334, N.336 Ligand excluded by PLIP NAG.22: 6 residues within 4Å: Chain D: Q.298, N.300, N.336, V.337, S.338, R.447 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain D: N.138, R.148 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain C: G.13, S.17 Chain D: E.92, N.93 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain E: S.17 Chain F: E.92, N.93 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain F: Q.135, S.155, F.156, N.157 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain F: Q.298, N.300, N.336 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain F: N.306, I.327, V.445 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain F: K.339, N.343, W.399 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain F: S.392, N.396 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain F: K.234, N.246 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain F: N.281, T.283, N.284 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain F: N.239, T.241, S.279, E.280 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cottrell, C.A. et al., Priming antibody responses to the fusion peptide in rhesus macaques. Npj Vaccines (2024)

Release Date

2024-05-22

Peptides

Surface protein gp120: ADF
Transmembrane protein gp41: BCE
NHP polyclonal antibody IF3 Heavy Chain: G
NHP polyclonal antibody IF3 Light Chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
E

F
F

B
B

C
C

E
D

G
H

H
L

Surface protein gp120

Transmembrane protein gp41

NHP polyclonal antibody IF3 Heavy Chain

NHP polyclonal antibody IF3 Light Chain

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