SMTL ID : 5cay.1

Envelope glycoprotein gp120 core from HIV type 2 bound to the first two domains of human soluble CD4 receptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-1-mer

Ligands

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

NAG-NAG.1: 8 residues within 4Å: Chain A: D.155, N.156, K.209, G.210, G.307, E.309 Chain B: E.88, K.91 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.91

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.2: 9 residues within 4Å: Chain A: Y.85, Q.131, N.139, T.235, N.236, R.238, C.294, N.295, S.296 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.295 Hydrogen bonds: A:R.238, A:R.238, A:N.295

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

NAG.3: 2 residues within 4Å: Chain A: N.46, K.332 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.332, A:K.332 NAG.4: 6 residues within 4Å: Chain A: E.33, I.34, A.35, N.105, K.118, V.120 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.120 Hydrogen bonds: A:N.105, A:K.118 NAG.5: 5 residues within 4Å: Chain A: E.224, A.231, Y.232, N.245, T.247 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:E.224, A:A.231, A:Y.232 Hydrogen bonds: A:E.224, A:N.245, A:T.247 NAG.6: 1 residues within 4Å: Chain A: N.167 No protein-ligand interaction detected (PLIP) NAG.7: 5 residues within 4Å: Chain A: N.145, N.163, F.165, Y.166, E.197 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.145, A:N.163, A:E.197 NAG.8: 4 residues within 4Å: Chain A: N.73, T.74 Chain B: S.61, D.64 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.64, A:N.73

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Davenport, Y.W. et al., Structure of an HIV-2 gp120 in Complex with CD4. J.Virol. (2015)

Release Date

2015-12-09

Peptides

Envelope glycoprotein gp120 core from ST strain of HIV-2: A
T-cell surface glycoprotein CD4: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
B

Envelope glycoprotein gp120 core from ST strain of HIV-2

T-cell surface glycoprotein CD4