SMTL ID : 9ays.1

HIV BG505.v5.2 (N289/N241) SOSIP Env in Complex with V5, gp120-Interface, and Anti-Immune Complex pAbs from Rh.33203

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

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

Ligands

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.1: 3 residues within 4Å: Chain C: N.153, Y.170, D.325 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.170

15 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 3 residues within 4Å: Chain C: F.156, N.157, K.168 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain C: H.90, K.234, N.246, V.247, S.248 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain C: Q.298, N.300, N.336, S.338 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: N.390, S.392 Ligands: NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain C: N.300, T.302, R.331, H.334, N.336, S.416 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain E: V.139, N.153, Y.170, L.172, D.325 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain E: N.300, T.302, H.334, N.336 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain E: N.367, S.368, S.369 Ligands: NAG.45 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain E: S.296, V.449, S.450, N.451 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain E: H.90, K.234, N.246, V.247, S.248 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 2 residues within 4Å: Chain F: N.102, T.104 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain G: N.281, T.283, N.284 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain G: N.300, H.334, N.336 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain G: V.139, N.141, N.153, Y.170, D.325 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.170 NAG-NAG.22: 3 residues within 4Å: Chain G: N.396, S.397, V.405 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 3 residues within 4Å: Chain C: R.197, N.202, T.203 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain E: V.179, R.197, I.199, N.200, N.202, T.203 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.179

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)][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.5: 10 residues within 4Å: Chain C: S.214, E.216, P.217, V.259, L.266, N.267, Q.443, R.447, V.449, S.450 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.449 Hydrogen bonds: C:R.447

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.11: 8 residues within 4Å: Chain E: E.216, V.259, L.266, N.267, G.383, C.448, V.449, S.450 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.17: 8 residues within 4Å: Chain G: K.69, L.266, N.267, C.382, R.447, C.448, V.449, S.450 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:V.449 Hydrogen bonds: G:K.69, G:K.69, G:V.449, G:Q.443

1 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.20: 5 residues within 4Å: Chain G: N.367, S.368, T.376, N.390 Ligands: NAG.59 No protein-ligand interaction detected (PLIP)

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

NAG.23: 2 residues within 4Å: Chain C: E.92, N.93 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: N.138, K.152, N.193 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: W.101, N.239, T.241, S.279 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: N.281, N.284 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.306, I.327, V.445 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: A.340, N.343, S.413 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: N.359, S.401, T.403, S.404 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain C: N.367, S.368, N.390, S.392 Ligands: NAG-NAG.7, NAG-NAG.7 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain C: S.392, N.396 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: Q.298, V.449, S.450, N.451 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: E.273, N.294, E.295 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain D: N.102, S.103, T.104 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain D: K.124, E.125, I.126, S.127, N.128 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain E: E.92, N.93 Chain F: G.18, S.19 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain E: T.137, N.138 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain E: N.141, N.142 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain E: F.156, N.157, K.166, Q.167, K.168 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain E: N.281, T.283 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain E: Q.298, N.300, N.336, V.337, S.338 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain E: N.306, I.327, V.445 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain E: N.343, W.399 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain E: R.354, K.355, N.359 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain E: N.390, S.392, R.422 Ligands: NAG-NAG.13, NAG-NAG.13 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain E: S.392, G.393, N.396 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain E: E.274, N.294, E.295 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain E: W.101, N.239, T.241, S.279, I.282 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain F: K.124, E.125, S.127, N.128 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain F: N.107, R.108, N.109 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain G: E.92, N.93 Chain H: G.18, S.19 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain G: S.155, F.156, N.157, K.168 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain A: X.54 Chain C: R.313 Chain G: R.197, N.202 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain G: N.239, T.241, S.279 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain G: E.272, E.273, N.294, E.295, K.348 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain G: Q.298, N.300, R.447 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain G: N.306, I.327, V.445 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain G: R.354, G.358, N.359 Ligand excluded by PLIP NAG.59: 6 residues within 4Å: Chain G: T.376, N.390, S.392 Ligands: NAG-NAG-NAG.20, NAG-NAG-NAG.20, NAG-NAG-NAG.20 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain G: V.449, S.450, N.451 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain G: S.463, T.464, N.465 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain G: H.90, N.246 Ligand excluded by PLIP NAG.63: 4 residues within 4Å: Chain G: A.340, N.343, T.403, T.411 Ligand excluded by PLIP NAG.64: 4 residues within 4Å: Chain H: P.100, W.101, 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

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

NHP gp120-Interface Epitope pAb - Predicted Heavy Chain: A
NHP gp120-Interface Epitope pAb - Predicted Light Chain: B
Surface protein gp120: CEG
Transmembrane protein gp41: DFH
NHP V5 Epitope pAb - Predicted Light Chain: I
NHP V5 Epitope pAb - Predicted Heavy Chain: J
NHP Anti-Immune Complex pAb - Predicted Heavy Chain: K
NHP Anti-Immune Complex pAb - Predicted Light Chain: L

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

E
C

G
E

D
B

F
D

H
F

I
G

J
I

K
J

L
K

NHP gp120-Interface Epitope pAb - Predicted Heavy Chain

NHP gp120-Interface Epitope pAb - Predicted Light Chain

Surface protein gp120

Transmembrane protein gp41

NHP V5 Epitope pAb - Predicted Light Chain

NHP V5 Epitope pAb - Predicted Heavy Chain

NHP Anti-Immune Complex pAb - Predicted Heavy Chain

NHP Anti-Immune Complex pAb - Predicted Light Chain

Related Entries With Identical Sequence