SMTL ID : 8fyj.1

Structure of HIV-1 BG505 SOSIP-HT2 in complex with two CD4 molecules (class I)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-2-1-3-2-mer

Ligands

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.1: 13 residues within 4Å: Chain A: S.177, P.180, L.229, N.230, N.344, C.345, I.405, G.407, V.408, I.409, C.411, V.412, S.413 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.177, A:V.408, A:E.179 Hydrophobic interactions: A:V.412 NAG-NAG-BMA-MAN.4: 13 residues within 4Å: Chain B: S.177, E.179, P.180, L.229, N.230, F.343, N.344, C.345, R.410, C.411, V.412, S.413 Ligands: NAG.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.179, B:S.177, B:C.345 NAG-NAG-BMA-MAN.8: 9 residues within 4Å: Chain C: K.220, N.230, N.344, C.345, G.346, I.405, R.410, C.411, V.412 No protein-ligand interaction detected (PLIP)

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.2: 5 residues within 4Å: Chain A: N.244, T.246, N.247, N.248, K.250 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.246

4 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG-NAG.3: 3 residues within 4Å: Chain A: N.330, N.353, S.355 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 2 residues within 4Å: Chain B: N.330 Ligands: NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: N.202, T.204, S.242, I.245 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: N.244, T.246 No protein-ligand interaction detected (PLIP)

1 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.5: 3 residues within 4Å: Chain B: N.244, T.246, N.247 No protein-ligand interaction detected (PLIP)

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

NAG.10: 4 residues within 4Å: Chain A: N.202, T.204, S.242, H.319 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.202 NAG.11: 4 residues within 4Å: Chain B: N.202, T.204, S.242, H.319 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain B: N.353, S.355 Ligands: NAG-NAG.6, NAG-NAG.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.355, B:S.355 NAG.13: 5 residues within 4Å: Chain B: K.220, N.230, P.259, N.414 Ligands: NAG-NAG-BMA-MAN.4 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.259 NAG.14: 2 residues within 4Å: Chain C: E.55, N.56 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:E.55 Hydrogen bonds: C:N.56 NAG.15: 6 residues within 4Å: Chain C: T.100, V.102, N.116, L.135, D.288, I.289 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.288, C:I.289 NAG.16: 4 residues within 4Å: Chain C: N.263, T.265, H.297, N.299 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.299

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dam, K.A. et al., Intermediate conformations of CD4-bound HIV-1 Env heterotrimers. Nature (2023)

Release Date

2023-10-18

Peptides

Envelope glycoprotein gp160: AB
Envelope glycoprotein gp160: C
Envelope glycoprotein gp41: DEF
T-cell surface glycoprotein CD4: GH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
Y

H
Z

Envelope glycoprotein gp160

Envelope glycoprotein gp160

Envelope glycoprotein gp41

T-cell surface glycoprotein CD4

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