SMTL ID : 3fus.1

Improved Structure of the Unliganded Simian Immunodeficiency Virus gp120 Core

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.00 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- BMA- FUL: beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-FUL.1: 4 residues within 4Å: Chain A: T.86, N.87, E.123, Y.129 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- FUL: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-FUL.2: 4 residues within 4Å: Chain A: Q.110, N.118, T.275 Ligands: NAG-NAG-BMA-FUL.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-FUL.10: 4 residues within 4Å: Chain A: N.84, D.85, T.86, N.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.85

1 x NAG- NAG- FUL: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUL.3: 4 residues within 4Å: Chain A: N.124, R.125, Y.144, K.176 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.125

1 x NAG- NAG- MAN- FUL: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-FUL.4: 3 residues within 4Å: Chain A: D.134, N.135, W.285 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- FUL: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-FUL.5: 3 residues within 4Å: Chain A: Y.144, N.146 Ligands: NAG-NAG-BMA-MAN-MAN-FUL.2 No protein-ligand interaction detected (PLIP)

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.6: 1 residues within 4Å: Chain A: N.184 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA- MAN- FUL: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-BMA-MAN-FUL.7: 5 residues within 4Å: Chain A: K.188, N.190, V.224 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.9, NAG-NAG-BMA-MAN.11 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- BMA- MAN- BMA- MAN: beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-beta-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-BMA-MAN-BMA-MAN.8: 5 residues within 4Å: Chain A: T.148, F.159, G.160, G.161, N.273 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.148 Hydrogen bonds: A:T.148, A:G.161

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.9: 2 residues within 4Å: Chain A: N.289 Ligands: NAG-NAG-BMA-BMA-MAN-FUL.7 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.11: 7 residues within 4Å: Chain A: T.192, A.193, P.194, D.284, N.289, N.292 Ligands: NAG-NAG-BMA-BMA-MAN-FUL.7 No protein-ligand interaction detected (PLIP)

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

NAG.12: 1 residues within 4Å: Chain A: N.7 No protein-ligand interaction detected (PLIP) NAG.13: 4 residues within 4Å: Chain A: N.52, T.53, S.54, I.55 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.52, A:I.55, A:I.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chen, X. et al., Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement. Acta Crystallogr.,Sect.D (2009)

Release Date

2009-06-30

Peptides

EXTERIOR MEMBRANE GLYCOPROTEIN GP120: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

EXTERIOR MEMBRANE GLYCOPROTEIN GP120

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