SMTL ID : 8g85.1

vFP52.02 Fab in complex with BG505 DS-SOSIP Env trimer

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

1 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.1: 10 residues within 4Å: Chain A: K.222, V.224, L.231, N.232, N.346, C.347, G.348, C.413, V.414, S.415 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348

12 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: 1 residues within 4Å: Chain A: N.265 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: T.267, H.299, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: N.332, T.341, N.355, S.357 Ligands: NAG-NAG.5, NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.4, NAG-NAG.4, NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: E.57, N.58 Chain D: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain C: T.267, H.299, N.301, S.381, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 8 residues within 4Å: Chain C: N.332, S.333, G.335, T.341, S.357 Ligands: NAG-NAG.13, NAG-NAG.13, NAG.42 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 6 residues within 4Å: Chain C: N.355, S.357, R.387 Ligands: NAG-NAG.12, NAG-NAG.12, NAG.42 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain E: Q.263, N.265, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain E: T.267, H.299, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 7 residues within 4Å: Chain E: N.332, S.333, G.335, T.341 Ligands: NAG-NAG-BMA.20, NAG-NAG-BMA.20, NAG.54 No protein-ligand interaction detected (PLIP)

1 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.6: 2 residues within 4Å: Chain A: P.261, N.416 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:Q.3

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.7: 3 residues within 4Å: Chain A: E.57, N.58 Chain B: S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.16: 6 residues within 4Å: Chain E: N.232, C.347, G.348, I.407, V.414, S.415 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.348

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.9: 6 residues within 4Å: Chain C: E.181, N.232, C.347, V.414, S.415 Ligands: NAG-NAG-BMA.14 No protein-ligand interaction detected (PLIP)

4 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.14: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.9 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 8 residues within 4Å: Chain E: E.57, N.58 Chain F: G.16, S.17 Chain H: T.31, Y.49, W.50, T.53 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:T.31 Hydrophobic interactions: H:T.53 NAG-NAG-BMA.20: 5 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG.19, NAG-NAG.19, NAG.54 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 2 residues within 4Å: Chain E: P.261, N.416 No protein-ligand interaction detected (PLIP)

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

NAG.22: 1 residues within 4Å: Chain A: N.103 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: V.104, N.106, N.118, D.290 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain A: T.98, Q.100, N.122 Chain E: D.129 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: R.162, N.167 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.246, T.248, N.249 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.271, I.292, V.410 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.5 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: N.204, T.206 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain B: N.100 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.126, Y.127 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.103, K.117 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain C: V.104, N.118, L.137 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: S.120, N.122 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: R.162, N.167, T.168 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: N.246, T.248, N.249 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: N.271, I.292, V.410 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.308, W.364 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.361 Ligands: NAG-NAG.12, NAG-NAG.13 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: N.204, T.206, S.244 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain D: P.98, N.100 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain D: N.126 Chain K: T.71, R.72 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain E: N.103, G.114 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain E: V.104, N.118 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain E: Q.100, N.122 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain E: N.167 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain E: N.246, T.248, N.249 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: N.271, I.292, V.410 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain E: N.308, W.364 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG.19, NAG-NAG-BMA.20 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain E: N.204, T.206, S.244 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain F: N.126, Y.127 Chain I: R.72 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sastry, M. et al., Diverse Murine Vaccinations Reveal Distinct Antibody Classes to Target Fusion Peptide and Variation in Peptide Length to Improve HIV Neutralization. J.Virol. (2023)

Release Date

2023-04-19

Peptides

Envelope glycoprotein gp120: ACE
Envelope glycoprotein gp41: BDF
vFP52.02 Heavy: GIK
vFP52.02 Light: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
D

E
J

B
B

D
E

F
K

G
H

I
A

K
F

H
L

J
C

L
I

Envelope glycoprotein gp120

Envelope glycoprotein gp41

vFP52.02 Heavy

vFP52.02 Light

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