SMTL ID : 3vq4.1

Fragments bound to HIV-1 integrase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

4 x CD: CADMIUM ION(Non-covalent)

CD.1: 4 residues within 4Å: Chain A: C.11, H.13, E.38 Ligands: CD.2 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.11, A:H.13, A:E.38, A:E.38 CD.2: 4 residues within 4Å: Chain A: C.11, E.38, D.62 Ligands: CD.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.11, A:E.38, A:D.62, H2O.1 CD.6: 4 residues within 4Å: Chain B: C.11, E.38, D.62 Ligands: CD.7 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.11, B:E.38, B:D.62, H2O.2, H2O.3 CD.7: 4 residues within 4Å: Chain B: C.11, H.13, E.38 Ligands: CD.6 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:C.11, B:H.13, B:E.38, H2O.4

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

SO4.3: 6 residues within 4Å: Chain A: E.15, K.17, R.112, E.116, H.117, L.118 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.15, A:L.118 Water bridges: A:K.17, A:K.17, A:K.119 Salt bridges: A:K.17, A:R.112, A:H.117

3 x 0NX: (5-phenyl-1,2-oxazol-3-yl)methanol(Non-covalent)

0NX.4: 10 residues within 4Å: Chain A: R.53, W.54, P.55, I.150, A.151, T.152 Chain B: H.131, G.143, E.144, D.148 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:P.55, A:I.150, B:E.144 Hydrogen bonds: A:T.152, B:E.144, B:D.148 0NX.5: 10 residues within 4Å: Chain A: Q.41, A.44, Y.45, L.48, T.71, A.74, A.75, W.78 Chain B: E.116, T.120 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:T.71, A:A.74, A:A.75, A:W.78, B:T.120 0NX.8: 10 residues within 4Å: Chain A: Y.29, N.130, H.131, G.143, E.144 Chain B: G.52, R.53, P.55, I.150, I.154 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.29, B:P.55 pi-Stacking: A:H.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wielens, J. et al., Parallel screening of low molecular weight fragment libraries: do differences in methodology affect hit identification?. J Biomol Screen (2013)

Release Date

2013-01-30

Peptides

POL polyprotein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

POL polyprotein

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