Arsenic in PDB 5krs: Hiv-1 Integrase Catalytic Core Domain in Complex with An Allosteric Inhibitor, 3-(1H-Pyrrol-1-Yl)-2-Thiophenecarboxylic Acid

The structure of Hiv-1 Integrase Catalytic Core Domain in Complex with An Allosteric Inhibitor, 3-(1H-Pyrrol-1-Yl)-2-Thiophenecarboxylic Acid, PDB code: 5krs was solved by D.Patel, J.D.Bauman, E.Arnold, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.95 / 1.70
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.908, 71.908, 67.684, 90.00, 90.00, 120.00
R / Rfree (%)	16.8 / 18.6

The binding sites of Arsenic atom in the Hiv-1 Integrase Catalytic Core Domain in Complex with An Allosteric Inhibitor, 3-(1H-Pyrrol-1-Yl)-2-Thiophenecarboxylic Acid (pdb code 5krs). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 2 binding sites of Arsenic where determined in the Hiv-1 Integrase Catalytic Core Domain in Complex with An Allosteric Inhibitor, 3-(1H-Pyrrol-1-Yl)-2-Thiophenecarboxylic Acid, PDB code: 5krs:
Jump to Arsenic binding site number: 1; 2;

Arsenic binding site 1 out of 2 in the Hiv-1 Integrase Catalytic Core Domain in Complex with An Allosteric Inhibitor, 3-(1H-Pyrrol-1-Yl)-2-Thiophenecarboxylic Acid


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Hiv-1 Integrase Catalytic Core Domain in Complex with An Allosteric Inhibitor, 3-(1H-Pyrrol-1-Yl)-2-Thiophenecarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:As65 b:22.3 occ:1.00 AS A:CAF65 0.0 22.3 1.0 O1 A:CAF65 1.6 31.2 1.0 CE1 A:CAF65 2.0 23.1 1.0 CE2 A:CAF65 2.0 73.6 1.0 SG A:CAF65 2.2 15.9 1.0 HE12 A:CAF65 2.5 27.7 1.0 HE11 A:CAF65 2.5 27.7 1.0 HE13 A:CAF65 2.5 27.7 1.0 HE21 A:CAF65 2.5 88.4 1.0 HE22 A:CAF65 2.5 88.4 1.0 HE23 A:CAF65 2.5 88.4 1.0 HB2 A:CAF65 3.0 23.7 1.0 H A:CAF65 3.0 17.4 1.0 CB A:CAF65 3.1 19.8 1.0 HG3 A:GLU92 3.5 25.4 1.0 HD21 A:ASN120 3.6 20.6 1.0 HA A:CAF65 3.6 20.7 1.0 N A:CAF65 3.7 14.5 1.0 ND2 A:ASN120 3.9 17.1 1.0 OD1 A:ASN120 3.9 18.3 1.0 CA A:CAF65 3.9 17.3 1.0 HB3 A:CAF65 3.9 23.7 1.0 CG A:ASN120 4.0 17.0 1.0 HG2 A:GLU92 4.2 25.4 1.0 H101 A:6XI302 4.2 22.0 1.0 OE1 A:GLU92 4.2 27.9 1.0 CG A:GLU92 4.2 21.2 1.0 C A:ASP64 4.2 17.6 1.0 HA A:ASP64 4.2 19.2 1.0 HG A:LEU74 4.3 25.9 1.0 OG1 A:THR97 4.3 14.5 1.0 HD22 A:ASN120 4.3 20.6 1.0 HG1 A:THR97 4.6 17.4 1.0 CD A:GLU92 4.6 30.9 1.0 HD12 A:LEU74 4.6 26.4 1.0 HB3 A:ASN120 4.8 16.1 1.0 CA A:ASP64 4.8 16.0 1.0 O A:ASP64 4.9 17.2 1.0 HD11 A:ILE89 4.9 24.3 1.0

Arsenic binding site 2 out of 2 in the Hiv-1 Integrase Catalytic Core Domain in Complex with An Allosteric Inhibitor, 3-(1H-Pyrrol-1-Yl)-2-Thiophenecarboxylic Acid


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Hiv-1 Integrase Catalytic Core Domain in Complex with An Allosteric Inhibitor, 3-(1H-Pyrrol-1-Yl)-2-Thiophenecarboxylic Acid within 5.0Å range: probe atom residue distance (Å) B Occ A:As130 b:33.2 occ:1.00 AS A:CAF130 0.0 33.2 1.0 O1 A:CAF130 1.6 36.0 1.0 CE1 A:CAF130 1.9 19.6 1.0 CE2 A:CAF130 2.0 46.2 1.0 SG A:CAF130 2.2 14.6 1.0 HE13 A:CAF130 2.4 23.6 1.0 HE12 A:CAF130 2.4 23.6 1.0 HE11 A:CAF130 2.4 23.6 1.0 HE23 A:CAF130 2.5 55.5 1.0 HE21 A:CAF130 2.5 55.5 1.0 HE22 A:CAF130 2.5 55.5 1.0 HB3 A:CAF130 2.8 17.4 1.0 CB A:CAF130 2.9 14.5 1.0 HB2 A:CAF130 3.0 17.4 1.0 HG12 A:VAL126 3.6 20.6 1.0 HA A:LYS127 3.9 15.2 1.0 HG21 A:VAL113 4.0 29.2 1.0 HA A:CAF130 4.1 18.1 1.0 HG22 A:VAL113 4.3 29.2 1.0 HB2 A:GLN137 4.3 36.7 1.0 HG23 A:VAL113 4.3 29.2 1.0 CG1 A:VAL126 4.3 17.2 1.0 HB3 A:PHE121 4.4 21.1 1.0 CG2 A:VAL113 4.4 24.3 1.0 CA A:CAF130 4.4 15.1 1.0 HG13 A:VAL126 4.4 20.6 1.0 HG22 A:ILE135 4.4 21.6 1.0 O A:VAL126 4.5 14.2 1.0 HG11 A:VAL126 4.5 20.6 1.0 H A:CAF130 4.6 19.7 1.0 HD13 A:LEU101 4.7 29.6 1.0 HG2 A:LYS127 4.7 26.6 1.0 O A:ILE135 4.7 16.8 1.0 HB A:ILE135 4.8 19.2 1.0 CA A:LYS127 4.8 12.7 1.0 HA A:GLN137 4.9 26.5 1.0 N A:CAF130 4.9 16.4 1.0 C A:VAL126 5.0 12.6 1.0 HG21 A:ILE135 5.0 21.6 1.0

D.Patel, J.Antwi, P.C.Koneru, E.Serrao, S.Forli, J.J.Kessl, L.Feng, N.Deng, R.M.Levy, J.R.Fuchs, A.J.Olson, A.N.Engelman, J.D.Bauman, M.Kvaratskhelia, E.Arnold. A New Class of Allosteric Hiv-1 Integrase Inhibitors Identified By Crystallographic Fragment Screening of the Catalytic Core Domain. J.Biol.Chem. V. 291 23569 2016.
ISSN: ESSN 1083-351X
PubMed: 27645997
DOI: 10.1074/JBC.M116.753384