SMTL ID : 9axi.1

HIV 16055.v8.3 SOSIP Env in Complex with Base and N625 Epitope pAbs from Rabbit 2463

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-1-1-1-1-3-mer

Ligands

17 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: 5 residues within 4Å: Chain H: V.184, R.198, N.203, T.204 Chain J: R.314 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain H: E.88, V.90, E.92, N.247 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:V.90 NAG-NAG.4: 7 residues within 4Å: Chain H: G.274, E.275, I.276, N.295, E.296, R.349, K.352 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:K.352 NAG-NAG.5: 5 residues within 4Å: Chain H: Q.367, T.376, T.377, N.390, S.392 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain H: S.392, N.396 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain H: N.268, S.297, N.451 Ligands: NAG-NAG-BMA-MAN-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain H: R.314 Chain I: V.184, R.198, N.203, T.204 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain I: N.236 Ligands: NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain I: N.240, G.241, S.280 Ligands: NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain I: V.90, E.92, N.247 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:V.90 NAG-NAG.14: 7 residues within 4Å: Chain I: G.274, E.275, I.276, N.295, E.296, R.349, K.352 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:K.352 NAG-NAG.15: 6 residues within 4Å: Chain I: Q.367, T.376, T.377, N.390, S.392 Ligands: NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain J: V.184, R.198, N.203, T.204 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:V.184 NAG-NAG.17: 5 residues within 4Å: Chain J: E.88, V.90, N.235, N.247 Ligands: NAG.47 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:V.90 NAG-NAG.19: 8 residues within 4Å: Chain J: G.274, E.275, I.276, N.295, E.296, R.349, K.352, K.353 1 PLIP interactions: 1 interactions with chain J Hydrophobic interactions: J:K.352 NAG-NAG.20: 6 residues within 4Å: Chain J: Q.367, T.376, T.377, N.390, S.392 Ligands: NAG.51 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain J: N.158, Y.175, L.177, G.325, D.326 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN: 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.3: 11 residues within 4Å: Chain H: T.215, D.217, V.260, L.267, N.268, N.381, R.383, C.448, K.449, S.450 Ligands: NAG-NAG.7 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:K.449 Hydrogen bonds: H:D.217, H:K.449 NAG-NAG-BMA-MAN-MAN.18: 11 residues within 4Å: Chain J: T.215, D.217, V.260, L.267, N.268, N.381, R.383, C.448, K.449, S.450 Ligands: NAG.53 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:D.217, J:K.449

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.8: 5 residues within 4Å: Chain I: V.139, N.158, Y.175, L.177, D.326 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:Y.175

1 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.13: 11 residues within 4Å: Chain I: T.215, D.217, V.260, L.267, N.268, N.381, R.383, K.449, S.450 Ligands: NAG.43, MAN.45 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:D.217, I:R.383, I:T.215, I:D.217

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

NAG.22: 2 residues within 4Å: Chain A: N.116, T.118 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: N.102, S.104 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: N.107 Chain E: X.98, X.99, X.100 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: R.124, E.125, N.128 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: N.102, S.103, S.104 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain C: N.102, S.104 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain C: N.116 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: S.104, W.105, S.106, N.107 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain H: V.139, N.158, Y.175, L.177, D.326 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain H: T.133, E.135, N.162 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain H: N.236, T.238, N.246 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain H: N.240, T.242, P.244, S.280 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain H: N.282, T.284, N.285 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain H: N.307, I.328 Ligands: NAG.36 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain H: T.303, N.445 Ligands: NAG.35 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain H: N.364, T.398, T.468, I.470 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain A: S.19 Chain H: E.92, N.93 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain I: T.133, S.160, F.161, N.162 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain I: N.282, T.284, N.285 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain I: S.392, N.396 Ligands: NAG-NAG.15 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain I: N.445 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain I: N.268, K.449, N.451 Ligands: NAG-NAG-BMA-MAN.13 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain I: N.307, I.328 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain I: N.364, T.398, I.470 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain J: N.236, N.246 Ligands: NAG-NAG.17 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain J: N.240, T.242, S.280 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain J: N.282, T.284, N.285 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain J: N.307, I.328, N.445 Ligands: NAG.52 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain J: S.392, N.396 Ligands: NAG-NAG.20 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain J: P.305, R.332, N.445 Ligands: NAG.50 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain J: N.268, S.297, N.451 Ligands: NAG-NAG-BMA-MAN-MAN.18 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain J: E.135, S.160, F.161, N.162 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain J: N.364, T.398, N.466, T.468, I.470 Ligand excluded by PLIP

1 x MAN: alpha-D-mannopyranose(Non-functional Binders)

MAN.45: 1 residues within 4Å: Ligands: NAG-NAG-BMA-MAN.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brown, S. et al., Anti-immune complex antibodies are elicited during repeated immunization with HIV Env immunogens. Sci Immunol (2025)

Release Date

2025-01-29

Peptides

Transmembrane protein gp41: ABC
Rabbit Polyclonal Antibody N625 Epitope - Predicted Light Chain: D
Rabbit Polyclonal Antibody N625 Epitope - Predicted Heavy Chain: E
Rabbit Polyclonal Antibody Base Epitope - Predicted Heavy Chain: F
Rabbit Polyclonal Antibody Base Epitope - Predicted Light Chain: G
Surface protein gp120: HIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
D

C
I

D
F

E
H

F
A

G
B

H
K

I
L

J
J

Transmembrane protein gp41

Rabbit Polyclonal Antibody N625 Epitope - Predicted Light Chain

Rabbit Polyclonal Antibody N625 Epitope - Predicted Heavy Chain

Rabbit Polyclonal Antibody Base Epitope - Predicted Heavy Chain

Rabbit Polyclonal Antibody Base Epitope - Predicted Light Chain

Surface protein gp120

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