SMTL ID : 8swx.1

BG505 Boost2 SOSIP.664 in complex with NHP polyclonal antibody Base4

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: 3 residues within 4Å: Chain A: E.92, N.93 Chain B: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.141, N.153, Y.170, L.172 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.170 NAG-NAG.4: 5 residues within 4Å: Chain D: V.139, N.153, Y.170, L.172, D.325 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Y.170

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, L.266, N.267, F.380, G.383, R.447, C.448, V.449, S.450 Ligands: NAG.19 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.449 Hydrogen bonds: A:V.449 NAG-NAG-BMA.5: 8 residues within 4Å: Chain D: E.216, L.266, N.267, N.381, G.383, V.449, S.450 Ligands: NAG.39 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.383 NAG-NAG-BMA.6: 11 residues within 4Å: Chain F: E.216, V.259, L.266, N.267, F.380, G.383, R.447, C.448, V.449, S.450 Ligands: NAG.61 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:V.449 Hydrogen bonds: F:V.449

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

NAG.7: 4 residues within 4Å: Chain A: C.136, T.137, N.138, R.148 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: N.141, N.142 Ligand excluded by PLIP NAG.9: 4 residues within 4Å: Chain A: S.155, F.156, N.157, K.168 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.202 Chain D: R.313 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain A: N.239, T.241, S.279 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: D.235, K.236, N.246 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain A: N.281, T.283, N.284 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain A: N.306, I.327 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: 5 residues within 4Å: Chain A: N.367, S.368, S.369, T.376 Ligands: NAG.18 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: T.376, 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: 4 residues within 4Å: Chain A: Q.298, N.300, R.447, V.449 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain A: E.272, E.273, E.274, N.294, K.348 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.343, S.397, W.399 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain A: N.396 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain B: N.100, T.102 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain B: N.107, S.109, E.110 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain B: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.100, T.102, I.130 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.126 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: S.17 Chain D: E.92, N.93 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain D: F.156, N.157, K.168 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain D: N.182, N.202, T.203 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain D: N.239, T.241, I.277, S.279, H.356 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain D: D.235, T.245, N.246 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: N.281, T.283 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain D: N.306, I.327, V.445 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain D: N.300, T.302, H.334, N.336, T.418 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain D: N.343, W.399 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain D: N.367, S.392, N.396 Ligands: NAG.43, NAG.44 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain D: N.267, S.296, N.451 Ligands: NAG-NAG-BMA.5 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain D: N.138, T.140, G.149 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain D: Q.298, N.300, S.416, R.447 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain D: N.359 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain D: N.390, S.392 Ligands: NAG.38 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain D: S.392, G.393, N.396 Ligands: NAG.38 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain E: N.100, T.102 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain E: N.107, S.109, E.110 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain E: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain E: S.17 Chain F: E.92, N.93 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain F: N.157 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain F: V.139, N.153, Y.170, L.172 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain A: R.313 Chain F: N.202, T.203 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain F: W.101, N.239, T.241, S.279 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain F: D.235, T.245, N.246 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain F: N.281, T.283 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain F: E.274, N.294, E.295 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain F: Q.298, N.300, N.336, S.338 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain F: N.306, I.327 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain F: N.300, T.302, H.334, N.336 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain F: N.343, W.399 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain F: T.376, N.390, S.392 Ligand excluded by PLIP NAG.61: 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

2024-05-22

Peptides

Surface protein gp120: ADF
Transmembrane protein gp41: BCE
Base4 Heavy Chain: G
Base4 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

Base4 Heavy Chain

Base4 Light Chain

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