SMTL ID : 8sw7.1

BG505 Boost2 SOSIP.664 in complex with NHP polyclonal antibody FP1

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

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.1: 10 residues within 4Å: Chain A: E.216, V.259, L.266, N.267, F.380, G.383, R.447, V.449, S.450 Ligands: NAG.17 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.449 NAG-NAG-BMA.2: 10 residues within 4Å: Chain C: P.217, L.266, N.267, N.381, C.382, G.383, R.447, V.449, S.450 Ligands: NAG.32 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.383, C:V.449 NAG-NAG-BMA.3: 11 residues within 4Å: Chain F: E.216, P.217, V.259, L.266, N.267, C.382, R.447, C.448, V.449, S.450 Ligands: NAG.52 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:V.449

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

NAG.4: 5 residues within 4Å: Chain A: E.92, N.93 Chain B: S.17 Chain G: X.57, X.58 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: C.136, T.137, N.138, K.152 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.142, G.328 Ligand excluded by PLIP NAG.7: 5 residues within 4Å: Chain A: V.139, N.141, N.153, L.172, D.325 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain A: N.157 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: V.179, R.197, N.202 Ligand excluded by PLIP NAG.10: 6 residues within 4Å: Chain A: N.239, T.241, S.279, E.280, N.281, I.282 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: 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: 3 residues within 4Å: Chain A: E.273, N.294, E.295 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.306, I.327, V.445 Ligand excluded by PLIP NAG.15: 5 residues within 4Å: Chain A: N.300, T.302, H.334, N.336, R.447 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: S.392, G.393, N.396 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain A: N.267, S.296, N.451 Ligands: NAG-NAG-BMA.1 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: Q.298, N.300, N.336, S.338, R.447 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.100, T.102 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.107, S.109, E.110 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain C: E.92, N.93 Chain E: G.13, S.17 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain C: N.138, T.140, R.148, K.152 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain C: V.139, N.141, N.153, L.172 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: S.155, F.156, N.157 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: W.101, N.239, T.241, S.279 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: D.235, T.245, N.246 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain C: E.272, E.273, N.294, E.295, K.348 Ligand excluded by PLIP NAG.28: 7 residues within 4Å: Chain C: Q.298, N.300, N.336, V.337, S.338, S.416, R.447 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: N.306, I.327, V.445 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain C: N.300, T.302, H.334, N.336 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: G.393, N.396 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: S.296, N.451 Ligands: NAG-NAG-BMA.2 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: S.368, T.376, N.390, S.392 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain D: P.98, W.99, N.100, T.102 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain D: E.123, N.126 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain E: N.100, T.102 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain E: N.107, S.109 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain E: K.122, E.123, I.124, S.125, N.126 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain F: N.93 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain F: C.136, N.138, K.194 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain F: V.139, N.153, Y.170, D.325 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain F: T.133, L.134, Q.135, S.155, F.156, N.157 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain F: W.101, N.239, T.241, S.279 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain F: K.234, T.245, N.246 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain F: N.281, T.283, N.284 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain F: E.272, E.273, N.294, E.295 Ligand excluded by PLIP NAG.47: 6 residues within 4Å: Chain F: Q.298, N.300, N.336, V.337, S.338, R.447 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain F: N.306, I.327 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain F: N.336, R.447 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain F: S.368, N.390, S.392 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain F: N.396 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain F: N.267, S.296, N.451 Ligands: NAG-NAG-BMA.3 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cottrell, C.A. et al., Focusing antibody responses to the fusion peptide in rhesus macaques. Biorxiv (2023)

Release Date

2023-07-26

Peptides

BG505 Boost 2 gp120: ACF
BG505 Boost 2 gp41: BDE
FP1 heavy chain: G
FP1 light chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

F
F

B
B

D
D

E
E

G
H

H
L

BG505 Boost 2 gp120

BG505 Boost 2 gp41

FP1 heavy chain

FP1 light chain

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