SMTL ID : 9ayv.1

HIV CH505/BG505 SOSIP.v8.1 Env in Complex with V1/V3 Epitope and Anti-Immune Complex pAbs from Rabbit 2474

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-3-3-2-1-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 E: A.139, T.140, N.152, N.169, L.171, Q.316 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain E: H.90, N.225, N.237, S.239 Ligands: NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain E: T.367, N.381, S.383 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain E: G.453, N.455 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain E: V.178, R.188, I.190, N.193 Chain G: R.304 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.178 NAG-NAG.8: 4 residues within 4Å: Chain E: N.226, T.228, N.236 Ligands: NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain F: N.297, I.318, V.436 Chain I: X.27 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain F: N.226 Ligands: NAG.40 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 1 residues within 4Å: Chain F: N.350 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain F: G.453, K.454, N.455 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain G: S.154, F.155, N.156, R.165 Ligands: NAG.47 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain G: N.226, T.228 Ligands: NAG.50 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain G: G.264, E.265, N.285, E.286 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain G: V.178, R.188, N.193 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:V.178

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.2: 4 residues within 4Å: Chain E: S.154, F.155, N.156, K.167 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 9 residues within 4Å: Chain E: E.207, P.208, V.250, L.257, N.258, G.374, V.440, S.441 Ligands: NAG.29 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.374, E:E.207 NAG-NAG-BMA.18: 10 residues within 4Å: Chain G: K.248, N.258, N.372, C.373, G.374, R.438, C.439, V.440, S.441 Ligands: NAG.56 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.438

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.10: 9 residues within 4Å: Chain A: X.88 Chain F: N.143 Chain H: X.88, X.89 Chain I: X.82, X.83 Chain J: X.57, X.61, X.62 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.11: 5 residues within 4Å: Chain E: D.163 Chain F: T.133, N.135, N.156 Ligands: NAG.38 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: 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.13: 8 residues within 4Å: Chain F: E.207, V.250, N.258, N.372, G.374, V.440, S.441 Ligands: NAG.35 No protein-ligand interaction detected (PLIP)

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

NAG.21: 2 residues within 4Å: Chain B: P.100, N.102 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain B: K.124, E.125, S.127, N.128 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: N.102, S.103, S.104 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain D: N.102 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain D: N.109, S.111, E.112 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain E: T.137, N.138 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain E: N.329, S.407 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain E: Q.357, P.358, N.387 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain E: N.258, S.287, N.442 Ligands: NAG-NAG-BMA.4 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain E: N.135, S.185, Q.186 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain E: N.350 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: N.297, I.318, V.436 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain F: N.329, T.332, N.405, D.406 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain F: T.368, N.381 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain F: N.258, S.287, N.442 Ligands: NAG-NAG-BMA-MAN.13 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain F: E.330, N.334, W.390 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: S.19 Chain F: E.92, N.93 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain F: N.135, Q.186 Ligands: NAG-NAG-BMA-MAN-MAN.11 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain F: R.188, N.193 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain F: N.225, N.237 Ligands: NAG-NAG.12 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain F: N.272, T.274, N.275 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain F: N.152, N.169, L.171, G.315, Q.316 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain F: E.265, N.285 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain F: N.138 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain F: P.358, N.387 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain D: A.16, S.19 Chain G: E.92, N.93 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain G: N.135, S.185, Q.186 Ligands: NAG-NAG.16 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain G: T.137, N.138 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain G: N.152, N.169, A.170, L.171, G.315 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain G: N.237 Ligands: NAG-NAG.17 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain G: N.297, I.318, V.436 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain G: N.329, N.405, D.406, S.407 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain G: N.334, L.337, W.390 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain G: N.350 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain G: P.358, S.383, N.387 Ligand excluded by PLIP NAG.56: 5 residues within 4Å: Chain G: N.258, V.440, S.441, N.442 Ligands: NAG-NAG-BMA.18 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain G: N.455 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain G: T.367, T.368, N.381, S.383 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

Rabbit Anti-Immune Complex pAb - Predicted Light Chain: A
Transmembrane protein gp41: BCD
Surface protein gp120: EFG
Rabbit V1/V3 Epitope pAb - Predicted Light Chain: HI
Rabbit V1/V3 Epitope pAb - Predicted Heavy Chain: J

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
J

B
B

C
D

D
F

E
A

F
C

G
N

H
H

I
G

J
E

Rabbit Anti-Immune Complex pAb - Predicted Light Chain

Transmembrane protein gp41

Surface protein gp120

Rabbit V1/V3 Epitope pAb - Predicted Light Chain

Rabbit V1/V3 Epitope pAb - Predicted Heavy Chain

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