SMTL ID : 8gpg.1

HIV-1 Env X18 UFO in complex with F6 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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: 5 residues within 4Å: Chain E: Q.1, Q.3, Y.25 Chain G: E.55, N.56 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.4: 7 residues within 4Å: Chain C: Q.1, Q.3, Y.25, G.26 Chain H: E.55, N.56 Ligands: NAG-NAG.6 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.25, C:Q.1, C:G.26 NAG-NAG-BMA-MAN-MAN.7: 5 residues within 4Å: Chain A: Q.1, Q.3, Y.25 Chain I: E.55, N.56 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 7 residues within 4Å: Chain G: D.188, V.231, N.239, N.351, R.353, T.411 Ligands: NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain F: L.61 Chain G: N.583 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain H: N.239, N.351, R.353, T.411 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain D: L.61 Chain H: N.583 Ligands: NAG-NAG-BMA-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 1 residues within 4Å: Chain I: N.583 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain I: D.188, V.231, N.239, N.351, R.353, S.412 Ligands: NAG.28 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:R.353, I:R.353

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

NAG.10: 4 residues within 4Å: Chain G: N.211, T.213, P.215, H.328 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain G: N.206, N.218 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain G: M.347, N.360, T.362 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain G: N.409 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain G: N.239, S.268, N.413 Ligands: NAG-NAG.2 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain G: N.569, T.571 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain G: N.315, E.374, F.375 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain H: N.211, T.213 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain H: N.206, N.218 Ligand excluded by PLIP NAG.19: 4 residues within 4Å: Chain H: L.343, M.347, N.360, T.362 Ligand excluded by PLIP NAG.20: 2 residues within 4Å: Chain H: S.272, N.409 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain H: S.268, N.413 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain H: N.569, S.570, T.571 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain H: N.315, N.319, E.374, F.375 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain I: N.211, S.251, L.254 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain I: N.206, N.218 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain I: N.360, T.362 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain I: E.308, N.409 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain I: S.268, N.413 Ligands: NAG-NAG.9, NAG-NAG.9 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain I: N.569, T.571 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain I: N.315, E.374, F.375 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niu, J. et al., Structures and immune recognition of Env trimers from two Asia prevalent HIV-1 CRFs. Nat Commun (2023)

Release Date

2023-08-09

Peptides

F6 Fab heavy chain: ACE
F6 Fab light chain: BDF
HIV-1 Env X18 UFO: GHI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
X

H
Y

I
Z

F6 Fab heavy chain

F6 Fab light chain

HIV-1 Env X18 UFO

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