SMTL ID : 8gas.1

vFP48.02 Fab in complex with BG505 DS-SOSIP Env trimer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

9 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: 6 residues within 4Å: Chain B: F.103, V.104 Chain C: E.57, N.58 Chain D: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 5 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG.4, NAG-NAG.4, NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 6 residues within 4Å: Chain F: F.103, V.104 Chain G: E.57, N.58 Chain H: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 5 residues within 4Å: Chain G: N.355, S.357 Ligands: NAG-NAG.11, NAG-NAG.11, NAG.42 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 4 residues within 4Å: Chain G: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 6 residues within 4Å: Chain J: F.103, V.104 Chain K: E.57, N.58 Chain L: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 5 residues within 4Å: Chain K: N.355, S.357 Ligands: NAG-NAG.18, NAG-NAG.18, NAG.54 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 4 residues within 4Å: Chain K: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.21 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 5 residues within 4Å: Chain C: Q.263, N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain C: T.267, N.301, S.381, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain C: N.332, S.333, G.335, T.341 Ligands: NAG-NAG-BMA.5, NAG-NAG-BMA.5, NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain G: Q.263, N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain G: T.267, N.301, S.381, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain G: N.332, S.333, G.335, T.341 Ligands: NAG-NAG-BMA.12, NAG-NAG-BMA.12, NAG.42 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain K: Q.263, N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain K: T.267, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 7 residues within 4Å: Chain K: N.332, S.333, G.335, T.341 Ligands: NAG-NAG-BMA.19, NAG-NAG-BMA.19, NAG.54 No protein-ligand interaction detected (PLIP)

3 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.7: 10 residues within 4Å: Chain C: S.179, V.224, L.231, N.232, C.347, R.412, C.413, V.414, S.415 Ligands: NAG-NAG-BMA.6 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.179, C:S.179 NAG-NAG-BMA-MAN.14: 9 residues within 4Å: Chain G: S.179, V.224, L.231, N.232, C.347, R.412, V.414, S.415 Ligands: NAG-NAG-BMA.13 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.179, G:S.179 NAG-NAG-BMA-MAN.21: 9 residues within 4Å: Chain K: S.179, V.224, L.231, N.232, C.347, R.412, V.414, S.415 Ligands: NAG-NAG-BMA.20 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:S.179, K:S.179

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

NAG.22: 1 residues within 4Å: Chain C: N.103 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: N.118, Y.135, L.137 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: T.98, N.122 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain C: R.162, N.167, T.168 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.246, T.248, N.249 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: N.271, I.292, G.409, V.410 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.308, W.364 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.361 Ligands: NAG-NAG.4, NAG-NAG-BMA.5 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: K.202, N.204, T.206 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain D: W.99, N.100 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: N.126, Y.127 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain G: N.103 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain G: N.118, Y.135, L.137 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain G: T.98, N.122 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain G: R.162, N.167 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain G: N.246, T.248, N.249 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain G: N.271, I.292, G.409, V.410 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain G: N.324 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain G: N.308, W.364 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain G: N.361 Ligands: NAG-NAG.11, NAG-NAG-BMA.12 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain G: K.202, N.204, T.206 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain H: W.99, N.100 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain H: N.126, Y.127 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain K: N.103, K.117 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain K: N.118, Y.135, L.137 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain G: D.129 Chain K: T.98, N.122 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain K: R.162, N.167, T.168 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain K: N.246, T.248, N.249 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain K: N.271, I.292, G.409, V.410 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain K: N.324 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain K: N.308, W.364 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain K: N.361 Ligands: NAG-NAG.18, NAG-NAG-BMA.19 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain K: K.202, N.204, T.206 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain L: W.99, N.100 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain L: N.126, Y.127 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sastry, M. et al., Diverse Murine Vaccinations Reveal Distinct Antibody Classes to Target Fusion Peptide and Variation in Peptide Length to Improve HIV Neutralization. J.Virol. (2023)

Release Date

2023-04-19

Peptides

vFP48.02 light chain: AEI
vFP48.02 heavy chain: BFJ
Envelope glycoprotein gp120: CGK
Envelope glycoprotein gp41: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

E
A

I
F

B
H

F
C

J
I

C
G

G
D

K
J

D
B

H
E

L
K

vFP48.02 light chain

vFP48.02 heavy chain

Envelope glycoprotein gp120

Envelope glycoprotein gp41

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