SMTL ID : 7lpn.1

Cryo-EM structure of llama J3 VHH antibody in complex with HIV-1 Env BG505 DS-SOSIP.664

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-mer

Ligands

6 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.1: 3 residues within 4Å: Chain B: N.118, Y.135, D.290 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.135 Hydrogen bonds: B:Y.135 NAG-NAG-BMA.2: 3 residues within 4Å: Chain B: R.162, N.167 Chain E: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain E: N.118, Y.135, D.290 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.135 Hydrogen bonds: E:Y.135 NAG-NAG-BMA.11: 3 residues within 4Å: Chain E: R.162, N.167 Chain H: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 4 residues within 4Å: Chain H: N.118, Y.135, L.137, D.290 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:Y.135 Hydrogen bonds: H:Y.135 NAG-NAG-BMA.20: 3 residues within 4Å: Chain B: R.278 Chain H: R.162, N.167 No protein-ligand interaction detected (PLIP)

15 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 B: N.204, T.206, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain B: T.267, H.299, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain B: N.355, S.357 Ligands: NAG-NAG.8, NAG.37 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: N.361 Ligands: NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain E: N.204, T.206, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain E: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain E: T.267, H.299, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG.17, NAG.48 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain H: N.204, T.206, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain H: N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain H: T.267, H.299, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain H: N.355, S.357 Ligands: NAG-NAG.26, NAG.59 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain H: N.361 Ligands: NAG-NAG.25 No protein-ligand interaction detected (PLIP)

3 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.5: 4 residues within 4Å: Chain B: N.271, I.292, V.410 Chain I: F.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.14: 4 residues within 4Å: Chain C: F.17 Chain E: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.23: 4 residues within 4Å: Chain F: F.17 Chain H: N.271, I.292, V.410 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.9: 7 residues within 4Å: Chain B: P.182, N.232, N.346, G.348, V.414, S.415 Ligands: NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.18: 7 residues within 4Å: Chain E: P.182, N.232, N.346, G.348, V.414, S.415 Ligands: NAG.47 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.27: 7 residues within 4Å: Chain H: P.182, N.232, N.346, G.348, V.414, S.415 Ligands: NAG.58 No protein-ligand interaction detected (PLIP)

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

NAG.28: 3 residues within 4Å: Chain A: N.100, S.102, W.103 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain A: N.126 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain B: E.57, N.58 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain B: N.103, G.114 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain B: N.246, T.248, N.249 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain B: N.308, W.364 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain B: K.316, N.324 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: N.106, N.107, G.293 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.9 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: N.332, T.341 Ligands: NAG-NAG.7, NAG-NAG.7 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain D: N.100, S.102, W.103 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain D: N.126 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain E: E.57, N.58 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain E: N.103, G.114 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain E: N.246, T.248, N.249 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain E: N.308 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain E: K.316, N.324 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain E: N.106, N.107, G.293 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain E: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.18 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain E: N.332, T.341 Ligands: NAG-NAG.16, NAG-NAG.16 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain E: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain G: N.100, S.102, W.103 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain G: N.126 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain H: E.57, N.58 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain H: N.103, G.114 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain H: N.246, T.248, N.249 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain H: N.308 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain H: K.316, N.324 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain H: N.106, N.107, G.293 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain H: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.27 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain H: N.332, T.341 Ligands: NAG-NAG.25, NAG-NAG.25 Ligand excluded by PLIP NAG.60: 5 residues within 4Å: Chain H: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, T. et al., Structural basis for llama nanobody recognition and neutralization of HIV-1 at the CD4-binding site. Structure (2022)

Release Date

2022-02-23

Peptides

HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41: ADG
Envelope glycoprotein gp160: BEH
J3 VHH: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

D
A

G
E

B
G

E
C

H
F

C
H

F
D

I
I

HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp41

Envelope glycoprotein gp160

J3 VHH

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