SMTL ID : 6met.1

Structural basis of coreceptor recognition by HIV-1 envelope spike

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-mer

Ligands

6 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.1: 1 residues within 4Å: Chain A: N.204 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain A: N.265 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.301, T.378 Ligands: NAG-NAG.5, NAG-NAG-BMA.7 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: F.341, N.354, T.356 Ligands: NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: K.222, N.232, P.261, D.263, N.413 No protein-ligand interaction detected (PLIP)

2 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.2: 3 residues within 4Å: Chain A: V.54, N.199, N.211 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 4 residues within 4Å: Chain A: P.269, N.271, Q.297 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP)

1 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.3: 15 residues within 4Å: Chain A: T.179, F.180, E.181, P.182, V.224, L.231, N.232, N.345, I.404, K.405, G.406, I.408, K.409, S.411, S.412 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.411

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

NAG.10: 2 residues within 4Å: Chain A: E.56, N.57 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.56 NAG.11: 4 residues within 4Å: Chain A: N.308, W.363, T.367, E.368 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.308, A:T.367, A:T.367 NAG.12: 1 residues within 4Å: Chain A: N.324 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.319, A:N.324 NAG.13: 2 residues within 4Å: Chain A: N.365, N.366 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.366 NAG.14: 2 residues within 4Å: Chain A: M.428, N.429 No protein-ligand interaction detected (PLIP) NAG.15: 2 residues within 4Å: Chain A: N.167, S.169 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.167 NAG.16: 2 residues within 4Å: Chain A: N.360 Ligands: NAG-NAG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.360

1 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Post Translational Modification)

A2G.17: 6 residues within 4Å: Chain A: Q.387, M.399 Chain C: Q.4, S.7, I.9, Y.10 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shaik, M.M. et al., Structural basis of coreceptor recognition by HIV-1 envelope spike. Nature (2018)

Release Date

2018-12-12

Peptides

Envelope glycoprotein gp160: A
T-cell surface glycoprotein CD4: B
C-C chemokine receptor type 5: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
A

C
B

Membrane

We predict this structure to be a membrane protein.
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Envelope glycoprotein gp160

T-cell surface glycoprotein CD4

C-C chemokine receptor type 5

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