SMTL ID : 3vqb.1

HIV-1 IN core domain in complex with 6-fluoro-4H-1,3-benzodioxine-8-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 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 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.11, A:H.13, A:E.38 CD.2: 4 residues within 4Å: Chain A: C.11, E.38, D.62 Ligands: CD.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:C.11, A:E.38, A:D.62, H2O.1, H2O.1 CD.5: 4 residues within 4Å: Chain B: C.11, E.38, D.62 Ligands: CD.6 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:C.11, B:E.38, B:D.62, H2O.2, H2O.2, H2O.3 CD.6: 4 residues within 4Å: Chain B: C.11, H.13, E.38 Ligands: CD.5 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:C.11, B:H.13, B:E.38, H2O.3, H2O.3

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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.15, A:L.118 Salt bridges: A:K.17, A:R.112, A:H.117

1 x FBG: 6-fluoro-4H-1,3-benzodioxine-8-carboxylic acid(Non-covalent)

FBG.4: 13 residues within 4Å: Chain A: Y.29, N.130, H.131, S.141, G.143, E.144, V.147 Chain B: G.52, R.53, W.54, P.55, I.150, I.154 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.130, A:S.141 Salt bridges: 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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