SMTL ID : 9axk.1

HIV 16055.v8.3 SOSIP Env in Complex with Base and N611 Epitope pAbs from Rabbit 2463

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

14 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: 6 residues within 4Å: Chain A: V.184, R.198, I.200, N.201, N.203, T.204 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.184 NAG-NAG.2: 4 residues within 4Å: Chain A: E.88, V.90, N.235, N.247 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.90 NAG-NAG.5: 3 residues within 4Å: Chain A: S.392, S.393, N.396 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.268, N.451 Ligands: NAG-NAG-BMA-MAN-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: V.184, R.198, N.203, T.204 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 8 residues within 4Å: Chain B: N.240, G.241, T.242, G.243, P.244, S.280, L.283 Ligands: NAG.32 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain B: Q.367, T.376, T.377, N.390, S.392 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.367 NAG-NAG.11: 3 residues within 4Å: Chain C: R.198, N.203, T.204 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: V.90, N.235, N.247 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.90 NAG-NAG.14: 6 residues within 4Å: Chain C: G.274, E.275, N.295, E.296, R.349, K.352 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:K.352 NAG-NAG.15: 4 residues within 4Å: Chain C: T.376, T.377, N.390, S.392 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: Q.367, S.392, S.393, N.396 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: N.158, Y.175, L.177, D.326 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain H: N.102, S.104 No protein-ligand interaction detected (PLIP)

3 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: 12 residues within 4Å: Chain A: R.71, T.215, D.217, P.218, V.260, L.267, N.268, R.383, C.448, K.449, S.450 Ligands: NAG-NAG.6 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.449 Hydrogen bonds: A:D.217, A:K.449, A:R.383 NAG-NAG-BMA-MAN-MAN.9: 11 residues within 4Å: Chain B: Y.66, T.215, D.217, L.267, N.268, N.381, C.382, R.383, K.449, S.450 Ligands: NAG.36 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:K.449 Hydrogen bonds: B:K.449 NAG-NAG-BMA-MAN-MAN.13: 9 residues within 4Å: Chain C: D.217, L.267, N.268, N.381, R.383, C.448, K.449, S.450 Ligands: NAG.45 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.449 Hydrogen bonds: C:K.449

1 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.4: 5 residues within 4Å: Chain A: E.275, I.276, N.295, E.296, R.349 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.349

31 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.19: 5 residues within 4Å: Chain A: N.158, Y.175, A.176, L.177, G.325 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain A: E.135, N.162 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: N.236, T.238, N.246, N.247 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.240, T.242, G.243, P.244 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.282, T.284, N.285 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: N.307, I.328, N.445 Ligands: NAG.27 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: N.364, T.468, I.470 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: T.376, T.377, N.390 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.445 Ligands: NAG.24 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain B: V.139, N.158, L.177, D.326 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain B: E.135, N.162 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain B: N.236, K.237, N.246 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: V.90, N.247 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.282, N.285 Ligands: NAG-NAG.8 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain B: G.274, E.275, I.276, N.295, E.296 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain B: S.392, S.393, N.396 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: P.305, N.445 Ligands: NAG.37 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain B: N.268, S.297, N.451 Ligands: NAG-NAG-BMA-MAN-MAN.9, NAG-NAG-BMA-MAN-MAN.9 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: N.307, I.328 Ligands: NAG.35 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.364, T.398, T.468 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: Q.348, N.400, N.402 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.236, K.237, P.244 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.240, T.242, S.280 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.282, T.284, N.285 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: N.307, I.328, N.445 Ligands: NAG.44 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain C: T.303, R.332, Y.335, N.445 Ligands: NAG.43 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: S.297, N.451 Ligands: NAG-NAG-BMA-MAN-MAN.13 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain C: E.92, N.93 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: S.160, F.161, N.162 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain J: N.102, S.104 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain J: N.116 Ligand excluded by 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

Surface protein gp120: ABC
Rabbit Base Epitope Polyclonal Antibody - Predicted Light Chain: D
Rabbit Base Epitope Polyclonal Antibody - Predicted Heavy Chain: E
Rabbit N611 Epitope Polyclonal Antibody - Predicted Light Chain: F
Rabbit N611 Epitope Polyclonal Antibody - Predicted Heavy Chain: G
Transmembrane protein gp41: HIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
M

B
D

C
I

D
F

E
H

F
A

G
B

H
N

I
C

J
J

Surface protein gp120

Rabbit Base Epitope Polyclonal Antibody - Predicted Light Chain

Rabbit Base Epitope Polyclonal Antibody - Predicted Heavy Chain

Rabbit N611 Epitope Polyclonal Antibody - Predicted Light Chain

Rabbit N611 Epitope Polyclonal Antibody - Predicted Heavy Chain

Transmembrane protein gp41

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