SMTL ID : 7rsn.1

AMC018 SOSIP.v4.2 in complex with PGV04 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 9 residues within 4Å: Chain A: N.254, F.255 Chain G: G.107 Chain H: Y.28, G.29, H.30, Q.64, F.65, G.66 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:G.66, H:Y.28, H:Q.64, H:Q.64 NAG-NAG-BMA-MAN-MAN.7: 9 residues within 4Å: Chain C: N.254, F.255 Chain I: G.107 Chain J: Y.28, G.29, H.30, Q.64, F.65, G.66 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:G.66, J:Y.28, J:Q.64, J:Q.64 NAG-NAG-BMA-MAN-MAN.13: 9 residues within 4Å: Chain E: N.254, F.255 Chain K: G.107 Chain L: Y.28, G.29, H.30, Q.64, F.65, G.66 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:G.66, L:Y.28, L:Q.64, L:Q.64

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.2: 9 residues within 4Å: Chain A: R.170, I.172, N.175, T.176, D.344 Chain G: K.12, S.17, D.77, L.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.344 Hydrophobic interactions: A:I.172 NAG-NAG-BMA-MAN-MAN-MAN.8: 9 residues within 4Å: Chain C: R.170, I.172, N.175, T.176, D.344 Chain I: K.12, S.17, D.77, L.78 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.344 Hydrophobic interactions: C:I.172 NAG-NAG-BMA-MAN-MAN-MAN.14: 9 residues within 4Å: Chain E: R.170, I.172, N.175, T.176, D.344 Chain K: K.12, S.17, D.77, L.78 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.344 Hydrophobic interactions: E:I.172

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.3: 4 residues within 4Å: Chain A: V.348, M.349, N.362 Ligands: NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 7 residues within 4Å: Chain A: N.127, Y.144, T.146, R.283, T.296, G.297, E.298 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.283 NAG-NAG.6: 4 residues within 4Å: Chain A: V.55, N.207, N.219 Ligands: NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain C: V.348, M.349, N.362 Ligands: NAG.31 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 7 residues within 4Å: Chain C: N.127, Y.144, T.146, R.283, T.296, G.297, E.298 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.283 NAG-NAG.12: 4 residues within 4Å: Chain C: V.55, N.207, N.219 Ligands: NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain E: V.348, M.349, N.362 Ligands: NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 7 residues within 4Å: Chain E: N.127, Y.144, T.146, R.283, T.296, G.297, E.298 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.283 NAG-NAG.18: 4 residues within 4Å: Chain E: V.55, N.207, N.219 Ligands: NAG.46 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.5: 9 residues within 4Å: Chain A: E.189, P.190, V.232, L.239, N.240, G.355, S.418, S.419 Ligands: NAG.25 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.355, A:S.418 NAG-NAG-BMA-MAN-MAN-MAN.11: 9 residues within 4Å: Chain C: E.189, P.190, V.232, L.239, N.240, G.355, S.418, S.419 Ligands: NAG.35 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.355, C:S.418 NAG-NAG-BMA-MAN-MAN-MAN.17: 9 residues within 4Å: Chain E: E.189, P.190, V.232, L.239, N.240, G.355, S.418, S.419 Ligands: NAG.45 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.355, E:S.418

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

NAG.19: 1 residues within 4Å: Chain A: N.435 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.131 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: Q.339, N.368 Ligands: NAG-NAG.3 Ligand excluded by PLIP NAG.22: 4 residues within 4Å: Chain A: N.273, T.275, H.307, N.309 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: E.271, N.273, S.418 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain A: N.279, I.300 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain A: N.240, S.269, N.420 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.5 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain A: N.208 Ligands: NAG-NAG.6 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain A: N.100, N.168 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.332 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.435 Ligand excluded by PLIP NAG.30: 1 residues within 4Å: Chain C: N.131 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: Q.339, N.368 Ligands: NAG-NAG.9 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain C: N.273, T.275, H.307, N.309 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: E.271, N.273, S.418 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.279, I.300 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: N.240, S.269, N.420 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.11 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: N.208 Ligands: NAG-NAG.12 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.100, N.168 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain C: N.332 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain E: N.435 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain E: N.131 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain E: Q.339, N.368 Ligands: NAG-NAG.15 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain E: N.273, T.275, H.307, N.309 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain E: E.271, N.273, S.418 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: N.279, I.300 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain E: N.240, S.269, N.420 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.17 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain E: N.208 Ligands: NAG-NAG.18 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain E: N.100, N.168 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain E: N.332 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schorcht, A. et al., The Glycan Hole Area of HIV-1 Envelope Trimers Contributes Prominently to the Induction of Autologous Neutralization. J.Virol. (2022)

Release Date

2021-09-15

Peptides

AMC018 gp120: ACE
AMC018 gp41: BDF
PGV04 Fab heavy chain: GIK
PGV04 kappa chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
G

B
B

D
D

F
I

G
H

I
E

K
F

H
L

J
J

L
K

AMC018 gp120

AMC018 gp41

PGV04 Fab heavy chain

PGV04 kappa chain

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