SMTL ID : 8f9g.1

HIV Env germline targeting BG505_MD64_N332-GT5 SOSIP in complex with V3-glycan polyclonal Fab isolated from immunized BG18HCgl knock-in mice

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

4 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.1: 11 residues within 4Å: Chain A: N.265, T.267, H.294, H.299, N.301, I.383 Chain G: X.103, X.104, X.105, X.106, X.107 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.4: 9 residues within 4Å: Chain A: S.179, E.181, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.179, A:S.179, A:G.348 NAG-NAG-BMA-MAN.6: 11 residues within 4Å: Chain C: S.179, E.181, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG.33 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.179, C:S.179, C:G.348, C:V.414 NAG-NAG-BMA-MAN.11: 10 residues within 4Å: Chain E: S.179, E.181, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.348, E:V.414

9 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: 5 residues within 4Å: Chain A: N.118, Y.135, L.137, G.289, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: R.162, I.164, N.167, T.168 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.164 NAG-NAG.5: 4 residues within 4Å: Chain C: N.118, Y.135, G.289, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: N.246, T.248, N.249 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:T.248 NAG-NAG.8: 6 residues within 4Å: Chain C: N.265, T.267, H.299, N.301, I.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain E: N.118, Y.135, G.289, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain E: V.144, R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain E: N.246, T.248, N.249 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:T.248 NAG-NAG.13: 6 residues within 4Å: Chain E: N.265, T.267, H.299, N.301, I.383, R.412 No protein-ligand interaction detected (PLIP)

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

NAG.14: 3 residues within 4Å: Chain A: E.57, N.58 Chain B: S.17 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain A: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.16: 4 residues within 4Å: Chain A: N.204, T.206, S.244, H.321 Ligand excluded by PLIP NAG.17: 5 residues within 4Å: Chain A: Q.263, N.265, N.301, S.303, R.412 Ligand excluded by PLIP NAG.18: 3 residues within 4Å: Chain A: N.271, L.292, V.410 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain A: L.338, T.341, T.342, N.355, S.357 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN.4 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain A: N.246, T.248, N.249 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: E.57, N.58 Chain D: S.17 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.204, T.206, S.244 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain C: Q.263, N.265, N.301, R.412 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: N.271, L.292, V.410 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: N.308, W.364 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain C: T.341, T.342, N.355, S.357 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: Q.332, N.361 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain C: P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN.6 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: R.278 Chain C: R.162, N.167, T.168 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain D: N.100, S.102 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain E: E.57, N.58 Chain F: S.17 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain E: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain E: N.204, T.206, S.244, H.321 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain E: Q.263, N.265, N.301, S.303 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain E: N.271, L.292, V.410 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain E: N.308, W.364 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain E: T.341, T.342, N.355, S.357 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: S.357, N.361 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: P.261, V.414, N.416 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain F: N.100, S.101, S.102 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xie, Z. et al., mRNA-LNP HIV-1 trimer boosters elicit precursors to broad neutralizing antibodies. Science (2024)

Release Date

2024-05-15

Peptides

BG505_MD64_N332-GT5 gp120: ACE
BG505_MD64_N332-GT5 gp41: BDF
V3-glycan epitope polyclonal Fab heavy chain: G
V3-glycan epitope polyclonal Fab light chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
E

E
F

B
B

D
G

F
I

G
H

H
L

BG505_MD64_N332-GT5 gp120

BG505_MD64_N332-GT5 gp41

V3-glycan epitope polyclonal Fab heavy chain

V3-glycan epitope polyclonal Fab light chain

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