SMTL ID : 9axd.1

HIV BG505.v5.2 (N289/N241) SOSIP Env in Complex with gp120-Interface pAb from Rh.33203

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-3-mer

Ligands

23 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: 3 residues within 4Å: Chain C: V.139, N.153, Y.170 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain C: N.281, T.283 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: Q.298, N.300, N.336, S.338 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: T.302, H.334, N.336, S.416 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain E: N.141, N.153, S.155, Y.170, D.325 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain E: T.133, Q.135, S.155, F.156, N.157 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain E: V.179, R.197, N.202, T.203 Chain G: R.313 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain E: N.239, T.241, G.242, S.279, H.356 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain E: K.234, N.246 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain E: E.273, N.294, K.348 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain E: Q.298, N.300, N.336, S.338 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain E: T.302, H.334, N.336, T.418 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain E: N.367, S.368, T.376, N.390 Ligands: NAG-NAG.17, NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain E: N.390, S.392 Ligands: NAG-NAG.16, NAG-NAG.16, NAG.49 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain E: S.296, N.451 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 2 residues within 4Å: Chain G: N.153, Y.170 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain G: N.239, S.279 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 2 residues within 4Å: Chain G: K.234, N.246 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain G: N.281, T.283, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain G: N.300, T.302, H.334, N.336, T.418 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 6 residues within 4Å: Chain G: N.367, S.368, T.376, N.390 Ligands: NAG-NAG.26, NAG-NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain G: N.390, S.392 Ligands: NAG-NAG.25, NAG-NAG.25, NAG.62 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain G: E.92, N.93 Chain H: S.19 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.2: 8 residues within 4Å: Chain C: E.216, L.266, N.267, N.381, R.447, V.449, S.450 Ligands: NAG.40 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.12: 10 residues within 4Å: Chain E: K.70, E.216, P.217, L.266, N.267, N.381, G.383, C.448, V.449, S.450 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.383 NAG-NAG-BMA-MAN-MAN.22: 10 residues within 4Å: Chain G: E.216, K.257, L.266, N.267, C.382, G.383, R.447, V.449, S.450 Ligands: NAG.63 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:V.449 Hydrogen bonds: G:G.383

1 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.6: 4 residues within 4Å: Chain C: N.367, S.368, N.390 Ligands: NAG.38 No protein-ligand interaction detected (PLIP)

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

NAG.28: 3 residues within 4Å: Chain C: E.92, N.93 Chain D: S.19 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: C.136, T.137, N.138, N.193 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: S.155, F.156, N.157 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: R.197, N.202 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: N.239, T.241, S.279, H.356 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain C: N.246 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.294, K.348 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: N.306, I.327, V.445 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain C: N.343 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: N.359, N.360, S.401 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain C: N.390, S.392 Ligands: NAG-NAG-NAG.6, NAG-NAG-NAG.6, NAG.39 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.396 Ligands: NAG.38 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain C: K.257, S.296, N.451 Ligands: NAG-NAG-BMA-MAN-MAN.2 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain D: N.102, T.104 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain D: N.128, Y.129 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain E: E.92, N.93 Chain F: S.19 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain E: N.138 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain E: N.142, I.327 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain E: N.281, T.283, N.284 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain E: N.306, I.327, V.445 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: K.339, N.343 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain E: N.396 Ligands: NAG-NAG.17 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain E: K.355, N.359 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain F: N.102, T.104 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain F: N.109, S.111, E.112 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain F: K.124, E.125, N.128 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain G: N.138, K.152 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain A: X.54 Chain C: R.313 Chain G: I.181, N.202, T.203 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain G: Q.135, S.155, F.156, N.157 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain G: E.273, E.274, N.294, E.295 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain G: Q.298, N.300, V.449 Ligand excluded by PLIP NAG.59: 2 residues within 4Å: Chain G: N.306, I.327 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain G: N.343, W.399, N.402 Ligand excluded by PLIP NAG.61: 4 residues within 4Å: Chain G: R.354, K.355, G.358, N.359 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain G: N.396 Ligands: NAG-NAG.26, NAG-NAG.26 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain G: S.296, N.451 Ligands: NAG-NAG-BMA-MAN-MAN.22 Ligand excluded by PLIP NAG.64: 2 residues within 4Å: Chain H: N.102, T.104 Ligand excluded by PLIP NAG.65: 3 residues within 4Å: Chain H: N.109, S.111, E.112 Ligand excluded by PLIP NAG.66: 1 residues within 4Å: Chain H: N.116 Ligand excluded by PLIP NAG.67: 2 residues within 4Å: Chain H: S.127, N.128 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

gp120-Interface Polyclonal Antibody - Predicted Heavy Chain: A
gp120-Interface Polyclonal Antibody - Predicted Light Chain: B
Surface protein gp120: CEG
Transmembrane protein gp41: DFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

E
C

G
E

D
B

F
D

H
F

gp120-Interface Polyclonal Antibody - Predicted Heavy Chain

gp120-Interface Polyclonal Antibody - Predicted Light Chain

Surface protein gp120

Transmembrane protein gp41

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