SMTL ID : 8t2e.1

BG505 Boost2 SOSIP.664 in complex with NHP polyclonal antibody FP3

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

3 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: 4 residues within 4Å: Chain A: E.92, N.93 Chain B: S.17 Chain G: X.75 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: V.139, N.153, Y.170, D.325 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.170 NAG-NAG.4: 5 residues within 4Å: Chain D: N.153, S.155, Y.170, L.172, D.325 No protein-ligand interaction detected (PLIP)

3 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.3: 10 residues within 4Å: Chain A: E.216, P.217, V.259, L.266, N.267, N.381, G.383, V.449, S.450 Ligands: NAG.19 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.449 Hydrogen bonds: A:G.383, A:V.449 NAG-NAG-BMA.5: 7 residues within 4Å: Chain D: E.216, L.266, N.267, G.383, V.449, S.450 Ligands: NAG.36 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.383 NAG-NAG-BMA.6: 9 residues within 4Å: Chain F: E.216, L.266, N.267, N.381, G.383, C.448, V.449, S.450 Ligands: NAG.56 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.383, F:V.449

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

NAG.7: 5 residues within 4Å: Chain A: C.136, T.137, N.138, K.152, Y.196 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain A: S.155, F.156, N.157 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.202, T.203, I.433 Ligand excluded by PLIP NAG.10: 6 residues within 4Å: Chain A: N.239, T.241, I.277, S.279, I.282, H.356 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: D.235, T.245, N.246 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.281, T.283, N.284 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain A: E.273, E.274, N.294, K.348 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.306, I.327, V.445 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: N.300, T.302, H.334, N.336 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain A: N.359 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.367, S.368 Ligands: NAG.18 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: T.377, N.390, S.392 Ligands: NAG.17 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain A: N.267, S.296, N.451 Ligands: NAG-NAG-BMA.3 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: S.392, N.396 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain A: Q.298, N.300, N.336, V.337, S.338, R.447 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain B: N.100, T.102 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.107, E.110 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain B: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain C: N.100, T.102 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: S.125, N.126 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: G.16, S.17 Chain D: E.92, N.93 Ligand excluded by PLIP NAG.28: 5 residues within 4Å: Chain D: Q.135, S.155, F.156, N.157, K.168 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain D: N.202, T.203 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain D: N.239, T.241, S.279, H.356 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain D: D.235, T.245, N.246 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain D: N.281, T.283, N.284 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: N.306, I.327 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain D: N.300, T.302, N.336 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain D: N.343, W.399 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain D: N.267, S.296, N.451 Ligands: NAG-NAG-BMA.5 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain D: N.300, S.338, R.447 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain D: N.390, S.392 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain B: A.1 Chain E: N.100, S.101 Chain H: X.52 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain E: N.105, R.106, N.107, E.110 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain E: E.123, N.126 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain E: S.17 Chain F: E.92, N.93 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain F: N.157 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain F: V.139, N.153, Y.170, L.172, D.325 Ligand excluded by PLIP NAG.45: 6 residues within 4Å: Chain F: N.239, T.241, I.277, S.279, I.282, H.356 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain F: D.235, T.245, N.246 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain F: N.281, T.283 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain F: E.272, E.273, N.294, E.295, K.348 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain F: Q.298, N.300, N.336, S.338 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain F: N.306, I.327, V.445 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain F: N.300, T.302, H.334, N.336 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain F: K.339, N.343, W.399 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain F: R.354, N.359 Ligand excluded by PLIP NAG.54: 5 residues within 4Å: Chain F: N.367, S.368, S.369, T.376 Ligands: NAG.55 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain F: N.390, S.392 Ligands: NAG.54 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain F: N.267, S.296, N.451 Ligands: NAG-NAG-BMA.6 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

2024-06-12

Peptides

Surface protein gp120: ADF
Transmembrane protein gp41: BCE
FP3 Heavy Chain: G
FP3 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

FP3 Heavy Chain

FP3 Light Chain

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