SMTL ID : 8g9w.1

Cryo-EM structure of vFP49.02 Fab in complex with HIV-1 Env BG505 DS-SOSIP.664 (conformation 1)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

21 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: 4 residues within 4Å: Chain C: E.57, N.58 Chain G: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain C: S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: R.162, I.164, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: N.204, S.244, E.245 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain C: Q.263, N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain A: S.17 Chain D: E.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain D: S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain D: R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain D: N.204, S.244, E.245 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 6 residues within 4Å: Chain D: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain D: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain D: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.19 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain B: S.17 Chain H: E.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain H: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain H: R.162, I.164, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain H: N.204, S.244, E.245 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain H: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain H: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 4 residues within 4Å: Chain H: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.32 No protein-ligand interaction detected (PLIP)

12 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.2: 5 residues within 4Å: Chain C: T.105, N.118, Y.135, L.137, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 6 residues within 4Å: Chain C: N.265, R.296, H.299, N.301, T.383, R.412 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.296, C:R.296 NAG-NAG-BMA.10: 7 residues within 4Å: Chain C: N.332, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 5 residues within 4Å: Chain C: S.357, G.358, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 4 residues within 4Å: Chain D: V.104, T.105, N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 5 residues within 4Å: Chain D: N.265, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 6 residues within 4Å: Chain D: N.332, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.25: 6 residues within 4Å: Chain D: S.357, G.358, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN.24, NAG-NAG-BMA-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 5 residues within 4Å: Chain H: V.104, T.105, N.118, Y.135, L.137 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 5 residues within 4Å: Chain H: N.265, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.36: 7 residues within 4Å: Chain H: N.332, T.341, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.37, NAG-NAG-BMA-MAN-MAN.37, NAG-NAG-BMA-MAN-MAN.37 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.38: 3 residues within 4Å: Chain H: G.358, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.37 No protein-ligand interaction detected (PLIP)

3 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: 7 residues within 4Å: Chain C: E.181, L.231, N.232, N.346, V.414, S.415 Ligands: NAG-NAG.13 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.181 NAG-NAG-BMA-MAN.19: 9 residues within 4Å: Chain D: E.181, V.224, L.231, N.232, N.346, C.413, V.414, S.415 Ligands: NAG-NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.32: 7 residues within 4Å: Chain H: L.231, N.232, N.346, C.413, V.414, S.415 Ligands: NAG-NAG.39 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.11: 7 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG-BMA.10, NAG-NAG-BMA.10, NAG-NAG-BMA.10, NAG-NAG-BMA.12, NAG-NAG-BMA.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.24: 8 residues within 4Å: Chain D: D.111, N.355, S.357 Ligands: NAG-NAG-BMA.23, NAG-NAG-BMA.23, NAG-NAG-BMA.23, NAG-NAG-BMA.25, NAG-NAG-BMA.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.37: 6 residues within 4Å: Chain H: N.355, S.357 Ligands: NAG-NAG-BMA.36, NAG-NAG-BMA.36, NAG-NAG-BMA.36, NAG-NAG-BMA.38 No protein-ligand interaction detected (PLIP)

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

NAG.40: 4 residues within 4Å: Chain A: K.122, E.123, N.126, Y.127 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain B: K.122, E.123, N.126 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.103, K.117, R.140 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.308 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain C: N.246, T.248 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain D: N.103, K.117, R.140 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain D: N.308, W.364 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain D: N.324 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: N.246, T.248 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain G: K.122, N.126, Y.127 Ligand excluded by PLIP NAG.51: 6 residues within 4Å: Chain H: N.103, R.113, K.117, R.140, K.159, Y.161 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain H: N.308, W.364 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain H: N.324 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain H: N.246, T.248 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 gp41: ABG
Envelope glycoprotein gp120: CDH
vFP49.02 heavy chain: E
vFP49.02 light chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

G
O

C
E

D
G

H
P

E
H

F
L

Envelope glycoprotein gp41

Envelope glycoprotein gp120

vFP49.02 heavy chain

vFP49.02 light chain

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