SMTL ID : 8sw7.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-3-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: 8 residues within 4Å: Chain C: E.216, L.266, N.267, R.447, C.448, V.449, S.450 Ligands: NAG.16 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.216, C:V.449 NAG-NAG-BMA.2: 11 residues within 4Å: Chain E: P.217, V.259, L.266, N.267, N.381, G.383, R.447, C.448, V.449, S.450 Ligands: NAG.31 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.383, E:V.449 NAG-NAG-BMA.3: 8 residues within 4Å: Chain H: E.216, V.259, L.266, N.267, G.383, V.449, S.450 Ligands: NAG.51 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:G.383

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

NAG.4: 5 residues within 4Å: Chain A: X.57, X.58 Chain C: E.92, N.93 Chain D: S.17 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain C: N.138 Ligand excluded by PLIP NAG.6: 3 residues within 4Å: Chain C: N.142, I.327, G.328 Ligand excluded by PLIP NAG.7: 5 residues within 4Å: Chain C: V.139, N.141, N.153, L.172, D.325 Ligand excluded by PLIP NAG.8: 1 residues within 4Å: Chain C: N.157 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain C: R.197, N.202 Ligand excluded by PLIP NAG.10: 5 residues within 4Å: Chain C: N.239, T.241, S.279, E.280, I.282 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: X.62 Chain C: D.235, T.245, N.246 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain C: N.281, T.283 Ligand excluded by PLIP NAG.13: 3 residues within 4Å: Chain C: E.274, N.294, E.295 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain C: N.306, I.327 Ligand excluded by PLIP NAG.15: 6 residues within 4Å: Chain C: N.300, T.302, H.334, N.336, T.418, R.447 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain C: N.267, N.451 Ligands: NAG-NAG-BMA.1 Ligand excluded by PLIP NAG.17: 6 residues within 4Å: Chain C: Q.298, N.300, N.336, V.337, S.338, R.447 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain C: T.376, N.390, S.392 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain D: N.100, T.102 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain D: N.107, S.109, E.110 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain D: N.126, Y.127 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain E: E.92, N.93 Chain G: S.17 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain E: N.138, K.152, Y.196 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain E: V.139, N.141, N.153, L.172 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain E: Q.135, F.156, N.157 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain E: N.239, T.241, S.279 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain E: E.272, E.273, N.294, E.295, K.348 Ligand excluded by PLIP NAG.28: 7 residues within 4Å: Chain E: 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 E: N.306, I.327, V.445 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain E: N.300, C.301, T.302, H.334, N.336, T.418 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain E: S.296, N.451 Ligands: NAG-NAG-BMA.2 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: N.281, T.283, N.284 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain E: N.390, S.392 Ligand excluded by PLIP NAG.34: 7 residues within 4Å: Chain E: V.179, I.181, L.198, I.199, N.200, N.202 Chain H: R.313 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain E: N.343, L.346, N.396, S.397, W.399 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain F: N.100, T.102 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain F: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain H: N.93 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain H: T.137, N.138, K.194 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain H: V.139, N.153, Y.170, D.325 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain H: Q.135, S.155, F.156, N.157 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain H: W.101, N.239, T.241, S.279 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain H: H.90, K.234, N.246 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain H: N.281, T.283, N.284 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain H: E.273, N.294, E.295, K.348 Ligand excluded by PLIP NAG.46: 6 residues within 4Å: Chain H: Q.298, N.300, N.336, V.337, S.338, R.447 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain H: N.306 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain H: N.300, T.302, N.336, R.447 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain H: T.377, N.390 Ligands: NAG.52 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain H: N.396 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain H: N.267, S.296, N.451 Ligands: NAG-NAG-BMA.3 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain H: N.367, S.368, S.369 Ligands: NAG.49 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

FP1 heavy chain: A
FP1 light chain: B
BG505 Boost 2 gp120: CEH
BG505 Boost 2 gp41: DFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

E
C

H
F

D
B

F
D

G
E

FP1 heavy chain

FP1 light chain

BG505 Boost 2 gp120

BG505 Boost 2 gp41

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