SMTL ID : 9atz.1

HIV 16055.v8.3 SOSIP Env in Complex with V2 Epitope and Anti-Immune Complex pAbs from Rabbit 2464

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-3-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 D: N.158, Y.175, L.177, D.326 Chain H: X.74, X.75 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain D: V.184, R.198, N.203, T.204 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain D: V.90, N.235, N.247 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.235 NAG-NAG.5: 6 residues within 4Å: Chain D: G.274, E.275, N.295, E.296, R.349, K.352 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:K.352 NAG-NAG.6: 4 residues within 4Å: Chain D: N.364, T.398, T.468, I.470 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain D: Q.367, N.390, S.392 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain I: V.90, N.235, N.236, K.237, N.247 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:N.235 NAG-NAG.10: 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.11: 4 residues within 4Å: Chain I: N.364, T.398, T.468, I.470 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain I: Q.367, N.390, S.392 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain M: E.275, I.276, N.295, E.296, R.349, K.352 1 PLIP interactions: 1 interactions with chain M Hydrophobic interactions: M:K.352 NAG-NAG.15: 5 residues within 4Å: Chain M: N.364, T.398, T.468, I.470 Ligands: NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain M: Q.367, P.368, T.376, T.377, N.390, S.392 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:Q.367 NAG-NAG.17: 5 residues within 4Å: Chain M: V.139, N.158, Y.175, L.177, D.326 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.4: 12 residues within 4Å: Chain D: T.215, D.217, K.258, V.260, L.267, N.268, R.383, T.447, C.448, K.449, S.450 Ligands: NAG.26 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:D.217 Hydrogen bonds: D:T.215, D:D.217 NAG-NAG-BMA-MAN-MAN.9: 9 residues within 4Å: Chain I: D.217, V.260, L.267, N.268, N.381, R.383, K.449, S.450 Ligands: NAG.36 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:D.217 NAG-NAG-BMA-MAN-MAN.13: 11 residues within 4Å: Chain M: T.215, D.217, V.260, L.267, N.268, N.381, R.383, C.448, K.449, S.450 Ligands: NAG.46 3 PLIP interactions: 3 interactions with chain M Hydrogen bonds: M:D.217, M:R.383, M:K.449

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

NAG.18: 3 residues within 4Å: Chain A: X.96 Chain D: R.190, N.193 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain D: N.307, I.328 Ligands: NAG.25 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain D: T.133, E.135, S.160, F.161, N.162 Ligand excluded by PLIP NAG.21: 5 residues within 4Å: Chain D: N.236, K.237, T.238, N.240, N.246 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain D: N.240, T.242, S.280 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain D: N.282, T.284, N.285 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain D: S.392, S.393, N.396 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain D: P.305, N.445 Ligands: NAG.19 Ligand excluded by PLIP NAG.26: 5 residues within 4Å: Chain D: N.268, K.449, S.450, N.451 Ligands: NAG-NAG-BMA-MAN-MAN.4 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain F: X.96 Chain I: R.190, N.193 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain I: N.307, I.328 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain I: N.158, Y.175, L.177, D.326 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain I: T.133, S.160, F.161, N.162 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain I: N.236, K.237, T.238, N.240 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain I: N.240, T.242, S.280 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain I: N.282, T.284, N.285 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain I: S.392, S.393, N.396 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain I: R.198, N.203, T.204 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain I: N.268, N.451 Ligands: NAG-NAG-BMA-MAN-MAN.9 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain M: R.190, N.193 Chain N: X.96 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain M: N.307, T.309, I.328 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain M: T.133, E.135, S.160, F.161, N.162 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain M: N.282, T.284, N.285 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain M: S.392, S.393, N.396 Ligands: NAG-NAG.15 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain I: R.314 Chain M: R.198, N.203, T.204 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain M: E.88, V.90, N.235, N.247 Ligand excluded by PLIP NAG.44: 7 residues within 4Å: Chain M: W.101, N.240, G.241, T.242, G.243, P.244, S.280 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain M: N.236, T.238 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain M: N.268, N.451 Ligands: NAG-NAG-BMA-MAN-MAN.13 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 V2 Polyclonal Antibody - Predicted Light Chain: AFN
Rabbit Anti-Immune Complex Antibody - Predicted Light Chain: BGK
Rabbit V2 Polyclonal Antibody - Predicted Heavy Chain: CHL
Surface protein gp120: DIM
Rabbit Anti-Immune Complex Antibody - Predicted Heavy Chain: EJR
Transmembrane protein gp41: OPQ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

F
F

N
N

B
B

G
G

K
K

C
C

H
H

L
L

D
D

I
I

M
M

E
E

J
J

R
R

O
O

P
P

Q
Q

Rabbit V2 Polyclonal Antibody - Predicted Light Chain

Rabbit Anti-Immune Complex Antibody - Predicted Light Chain

Rabbit V2 Polyclonal Antibody - Predicted Heavy Chain

Surface protein gp120

Rabbit Anti-Immune Complex Antibody - Predicted Heavy Chain

Transmembrane protein gp41

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