SMTL ID : 3l3v.1

Structure of HIV-1 integrase core domain in complex with sucrose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.1: 12 residues within 4Å: Chain A: E.38, V.39, E.47, Y.50, K.54, K.124 Chain B: E.38, V.39, E.47, Y.50, K.54, K.124 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:E.38, A:E.47, A:Y.50, A:K.54, B:V.39, B:K.124, B:E.47, B:K.54, A:V.39, A:K.124, A:K.124 Water bridges: A:E.47, A:F.51, B:E.47

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: R.138, I.142 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.138 SO4.5: 6 residues within 4Å: Chain B: E.20, K.22, R.117, E.121, H.122, L.123 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.20, B:R.117, B:L.123 Water bridges: B:K.124 Salt bridges: B:K.22, B:H.122

4 x CD: CADMIUM ION(Non-covalent)

CD.3: 4 residues within 4Å: Chain A: C.16, H.18, E.43 Ligands: CD.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.16, A:H.18, A:E.43, H2O.1 CD.4: 4 residues within 4Å: Chain A: C.16, E.43, D.67 Ligands: CD.3 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.16, A:E.43, A:D.67, H2O.1, H2O.2 CD.6: 4 residues within 4Å: Chain B: C.16, E.43, D.67 Ligands: CD.7 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:C.16, B:E.43, H2O.2, H2O.3, H2O.4 CD.7: 4 residues within 4Å: Chain B: C.16, H.18, E.43 Ligands: CD.6 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.16, B:H.18, B:E.43, H2O.2, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wielens, J. et al., Crystal structure of the HIV-1 integrase core domain in complex with sucrose reveals details of an allosteric inhibitory binding site. Febs Lett. (2010)

Release Date

2010-03-31

Peptides

POL polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

POL polyprotein

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