SMTL ID : 6p62.1

HIV Env BG505 NFL TD+ in complex with antibody E70 fragment antigen binding

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

12 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: V.128, T.129, N.142, D.314 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: N.88, T.230, E.269, N.270 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.2, NAG-NAG-BMA-MAN-MAN-MAN-MAN.2 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain A: N.356, S.357, S.358, T.365, N.379 Ligands: NAG-NAG.6, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.379, S.381 Ligands: NAG-NAG.5, NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain D: V.128, T.129, N.142, D.314 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain D: N.88, T.230, E.269, N.270 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.8, NAG-NAG-BMA-MAN-MAN-MAN-MAN.8 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain D: N.356, S.357, S.358, T.365, N.379 Ligands: NAG-NAG.12, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain D: N.379, S.381 Ligands: NAG-NAG.11, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain G: V.128, T.129, N.142, D.314 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain G: N.88, T.230, E.269, N.270 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN-MAN-MAN.14 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 7 residues within 4Å: Chain G: N.356, S.357, S.358, T.365, N.379 Ligands: NAG-NAG.18, NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain G: N.379, S.381 Ligands: NAG-NAG.17, NAG-NAG.17 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.2: 14 residues within 4Å: Chain A: N.228, T.230, I.271, T.272, H.345 Chain B: G.31, Y.52, N.57, Y.59, S.104, V.105 Chain C: N.93 Ligands: NAG-NAG.4, NAG-NAG.4 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.57 NAG-NAG-BMA-MAN-MAN-MAN-MAN.8: 14 residues within 4Å: Chain D: N.228, T.230, I.271, T.272, H.345 Chain E: G.31, Y.52, N.57, Y.59, S.104, V.105 Chain F: N.93 Ligands: NAG-NAG.10, NAG-NAG.10 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.57 NAG-NAG-BMA-MAN-MAN-MAN-MAN.14: 14 residues within 4Å: Chain G: N.228, T.230, I.271, T.272, H.345 Chain H: G.31, Y.52, N.57, Y.59, S.104, V.105 Chain I: N.93 Ligands: NAG-NAG.16, NAG-NAG.16 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:N.57

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.3: 5 residues within 4Å: Chain A: P.206, L.255, N.256, V.438 Ligands: NAG.27 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.438 Hydrogen bonds: A:V.438 NAG-NAG-BMA-MAN.9: 5 residues within 4Å: Chain D: P.206, L.255, N.256, V.438 Ligands: NAG.36 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.438 Hydrogen bonds: D:V.438 NAG-NAG-BMA-MAN.15: 5 residues within 4Å: Chain G: P.206, L.255, N.256, V.438 Ligands: NAG.45 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:V.438 Hydrogen bonds: G:V.438

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

NAG.19: 4 residues within 4Å: Chain A: Q.124, S.144, F.145, N.146 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: V.168, R.186, N.191 Ligand excluded by PLIP NAG.21: 6 residues within 4Å: Chain A: Q.287, N.289, N.325, V.326, S.327, R.436 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.295, I.316, V.434 Ligand excluded by PLIP NAG.23: 5 residues within 4Å: Chain A: N.289, T.291, H.323, N.325, R.436 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: T.126, N.127 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: N.332, W.388 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.385 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: L.259, P.285, N.440 Ligands: NAG-NAG-BMA-MAN.3 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain D: Q.124, S.144, F.145, N.146 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain D: V.168, R.186, N.191 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain D: Q.287, N.289, N.325, V.326, S.327, R.436 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain D: N.295, I.316, V.434 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain D: N.289, T.291, H.323, N.325, R.436 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain D: T.126, N.127 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: N.332, W.388 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain D: N.385 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain D: L.259, P.285, N.440 Ligands: NAG-NAG-BMA-MAN.9 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain G: Q.124, S.144, F.145, N.146 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain G: V.168, R.186, N.191 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain G: Q.287, N.289, N.325, V.326, S.327, R.436 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain G: N.295, I.316, V.434 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain G: N.289, T.291, H.323, N.325, R.436 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain G: T.126, N.127 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain G: N.332, W.388 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain G: N.385 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain G: L.259, P.285, N.440 Ligands: NAG-NAG-BMA-MAN.15 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dubrovskaya, V. et al., Vaccination with Glycan-Modified HIV NFL Envelope Trimer-Liposomes Elicits Broadly Neutralizing Antibodies to Multiple Sites of Vulnerability. Immunity (2019)

Release Date

2019-11-20

Peptides

HIV-1 Env BG505 NFL TD+: ADG
Rabbit monoclonal antibody E70 heavy chain fragment antigen binding: BEH
Rabbit monoclonal antibody E70 kappa chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
B

G
E

B
H

E
C

H
F

C
L

F
D

I
G

HIV-1 Env BG505 NFL TD+

Rabbit monoclonal antibody E70 heavy chain fragment antigen binding

Rabbit monoclonal antibody E70 kappa chain