SMTL ID : 8fr6.1

Antibody vFP53.02 in complex with HIV-1 envelope trimer BG505 DS-SOSIP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 3 residues within 4Å: Chain C: N.103, K.117, R.140 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: R.162, N.167 Chain E: R.278 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.15: 3 residues within 4Å: Chain E: N.103, K.117, R.140 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain E: R.162, N.167 Chain F: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain E: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain F: N.103, K.117, R.140 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain C: R.278 Chain F: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 3 residues within 4Å: Chain F: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP)

6 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.2: 4 residues within 4Å: Chain C: N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.11: 5 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG-BMA.10, NAG-NAG-BMA.10, NAG-NAG-BMA.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.16: 4 residues within 4Å: Chain E: N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.25: 5 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG-BMA.24, NAG-NAG-BMA.24, NAG-NAG-BMA.28 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.30: 4 residues within 4Å: Chain F: N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.39: 5 residues within 4Å: Chain F: N.355, S.357 Ligands: NAG-NAG-BMA.38, NAG-NAG-BMA.38, NAG-NAG-BMA.42 No protein-ligand interaction detected (PLIP)

24 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.4: 6 residues within 4Å: Chain C: E.62, N.204, T.206, P.208, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain C: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 6 residues within 4Å: Chain C: Q.263, N.265, V.302, S.303, R.412 Ligands: NAG-NAG-BMA.9 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 8 residues within 4Å: Chain C: N.265, T.267, H.299, N.301, S.381, T.383, R.412 Ligands: NAG-NAG-BMA.7 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 6 residues within 4Å: Chain C: N.332, S.333, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.11, NAG-NAG-BMA-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 5 residues within 4Å: Chain C: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 4 residues within 4Å: Chain C: 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.18: 6 residues within 4Å: Chain E: E.62, N.204, T.206, P.208, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 3 residues within 4Å: Chain E: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 6 residues within 4Å: Chain E: Q.263, N.265, V.302, S.303, R.412 Ligands: NAG-NAG-BMA.23 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 8 residues within 4Å: Chain E: N.265, T.267, H.299, N.301, S.381, T.383, R.412 Ligands: NAG-NAG-BMA.21 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.24: 6 residues within 4Å: Chain E: N.332, S.333, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.25, NAG-NAG-BMA-MAN-MAN.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 4 residues within 4Å: Chain E: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.19 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 5 residues within 4Å: Chain E: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 4 residues within 4Å: Chain E: G.358, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.25, NAG-NAG-BMA-MAN-MAN.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.32: 6 residues within 4Å: Chain F: E.62, N.204, T.206, P.208, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.34: 3 residues within 4Å: Chain F: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 6 residues within 4Å: Chain F: Q.263, N.265, V.302, S.303, R.412 Ligands: NAG-NAG-BMA.37 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.37: 8 residues within 4Å: Chain F: N.265, T.267, H.299, N.301, S.381, T.383, R.412 Ligands: NAG-NAG-BMA.35 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.38: 6 residues within 4Å: Chain F: N.332, S.333, N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.39, NAG-NAG-BMA-MAN-MAN.39 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.40: 4 residues within 4Å: Chain F: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.33 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.41: 5 residues within 4Å: Chain F: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.42: 4 residues within 4Å: Chain F: G.358, N.361 Ligands: NAG-NAG-BMA-MAN-MAN.39, NAG-NAG-BMA-MAN-MAN.39 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.5: 13 residues within 4Å: Chain C: S.179, E.181, P.182, V.224, L.231, N.232, R.274, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG-BMA.12 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.181, C:V.414 NAG-NAG-BMA-MAN-MAN-MAN.19: 13 residues within 4Å: Chain E: S.179, E.181, P.182, V.224, L.231, N.232, R.274, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG-BMA.26 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:E.181, E:V.414 NAG-NAG-BMA-MAN-MAN-MAN.33: 13 residues within 4Å: Chain F: S.179, E.181, P.182, V.224, L.231, N.232, R.274, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG-BMA.40 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.181, F:V.414

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

NAG.43: 1 residues within 4Å: Chain A: N.100 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain A: N.107, E.110 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain A: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.100 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain B: N.107, E.110 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain B: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain C: N.58 Chain G: T.58 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain C: N.107 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.308 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain D: N.100 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain D: N.107, E.110 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain D: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain E: N.58 Chain I: T.58 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain E: N.107 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain E: N.308 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.60: 2 residues within 4Å: Chain F: N.58 Chain K: T.58 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain F: N.107 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain F: N.308 Ligand excluded by PLIP NAG.63: 1 residues within 4Å: Chain F: N.324 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: ABD
Envelope glycoprotein gp120: CEF
vFP53.02 Fab heavy chain: GIK
vFP53.02 Fab light chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
F

C
C

E
G

F
I

G
D

I
H

K
J

H
E

J
L

L
K

Envelope glycoprotein gp41

Envelope glycoprotein gp120

vFP53.02 Fab heavy chain

vFP53.02 Fab light chain

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