SMTL ID : 8gp5.1

Structure of X18 UFO protomer in complex with F6 Fab VHVL domain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

2 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: 6 residues within 4Å: Chain A: Q.1, Q.3, Q.5, Y.25, G.26 Chain C: N.56 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.5, A:Q.1 NAG-NAG-BMA-MAN-MAN.3: 8 residues within 4Å: Chain C: D.188, P.189, V.231, N.239, N.351, R.353, T.411, S.412 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.188, C:R.353

5 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: 3 residues within 4Å: Chain C: N.211, T.213, S.251 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain C: N.253, N.256 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain C: N.310, T.312, E.313 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: M.347, N.360, T.362 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: Q.1 Chain C: E.579, N.583 No protein-ligand interaction detected (PLIP)

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

NAG.8: 1 residues within 4Å: Chain C: N.218 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.218 NAG.9: 5 residues within 4Å: Chain C: E.245, E.246, I.247, N.266, K.324 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:I.247, C:N.266 NAG.10: 4 residues within 4Å: Chain C: N.239, G.240, L.242, N.413 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.242 NAG.11: 2 residues within 4Å: Chain C: N.315, N.319 No protein-ligand interaction detected (PLIP) NAG.12: 3 residues within 4Å: Chain C: S.272, E.308, N.409 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.409 NAG.13: 3 residues within 4Å: Chain C: N.569, T.571, R.599 No protein-ligand interaction detected (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 VH domain: A
F6 Fab VL domain: B
X18 UFO Env protomer: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

B
F

C
X

F6 Fab VH domain

F6 Fab VL domain

X18 UFO Env protomer

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