Chlorine in PDB 6bra: Hiv-1 Protease (D25N, Inactive) in Complex with Phage Display Optimized Substrate Sgiflets

The structure of Hiv-1 Protease (D25N, Inactive) in Complex with Phage Display Optimized Substrate Sgiflets, PDB code: 6bra was solved by I.W.Windsor, R.T.Raines, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	27.62 / 1.11
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	58.033, 85.767, 46.130, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 18.4

The binding sites of Chlorine atom in the Hiv-1 Protease (D25N, Inactive) in Complex with Phage Display Optimized Substrate Sgiflets (pdb code 6bra). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Hiv-1 Protease (D25N, Inactive) in Complex with Phage Display Optimized Substrate Sgiflets, PDB code: 6bra:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Hiv-1 Protease (D25N, Inactive) in Complex with Phage Display Optimized Substrate Sgiflets


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Hiv-1 Protease (D25N, Inactive) in Complex with Phage Display Optimized Substrate Sgiflets within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl101 b:12.0 occ:1.00 O A:HOH318 3.0 23.7 1.0 N A:THR74 3.2 8.9 1.0 ND2 A:ASN88 3.3 9.7 1.0 CA A:GLY73 3.8 10.7 1.0 OG1 A:THR74 3.8 12.2 1.0 CB A:THR74 3.9 10.4 1.0 CB A:ASN88 3.9 9.0 1.0 C A:GLY73 4.0 10.2 1.0 CG A:ASN88 4.1 8.8 1.0 CA A:THR74 4.2 9.7 1.0 O A:HOH241 4.4 15.1 1.0 O A:HOH233 4.5 32.8 1.0 O A:ASN88 4.6 8.9 1.0 O A:THR74 4.7 10.3 1.0 O A:HOH216 4.8 23.3 1.0 CA A:ASN88 4.9 8.4 1.0 C A:THR74 5.0 9.6 1.0

Chlorine binding site 2 out of 4 in the Hiv-1 Protease (D25N, Inactive) in Complex with Phage Display Optimized Substrate Sgiflets


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Hiv-1 Protease (D25N, Inactive) in Complex with Phage Display Optimized Substrate Sgiflets within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl102 b:29.8 occ:1.00 O A:HOH319 3.0 30.2 1.0 N A:THR12 3.2 13.7 1.0 CB A:VAL11 3.7 15.2 1.0 CB A:ALA67 3.8 19.9 1.0 CA A:VAL11 3.9 13.2 1.0 CB A:THR12 3.9 16.3 1.0 CA A:ALA67 3.9 16.8 1.0 O A:HOH252 4.0 30.3 1.0 C A:VAL11 4.1 12.0 1.0 OG1 A:THR12 4.1 18.2 1.0 CA A:THR12 4.1 13.0 1.0 O A:THR12 4.1 14.5 1.0 CG1 A:VAL11 4.3 17.7 1.0 C A:THR12 4.6 13.2 1.0 N A:ALA67 4.8 15.1 1.0 O A:HOH311 4.8 39.4 1.0 CG2 A:VAL11 4.9 16.3 1.0 C A:ALA67 5.0 19.7 1.0

Chlorine binding site 3 out of 4 in the Hiv-1 Protease (D25N, Inactive) in Complex with Phage Display Optimized Substrate Sgiflets


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Hiv-1 Protease (D25N, Inactive) in Complex with Phage Display Optimized Substrate Sgiflets within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl103 b:22.7 occ:1.00 O A:HOH235 3.0 23.5 1.0 O A:HOH330 3.1 30.1 1.0 N A:LYS55 3.3 10.9 1.0 CA A:ILE54 3.7 10.0 1.0 CB A:ILE54 3.8 12.7 1.0 O A:HOH265 3.9 38.7 1.0 C A:ILE54 4.0 10.2 1.0 CG2 A:ILE54 4.1 14.2 1.0 CB A:LYS55 4.1 12.1 1.0 CA A:LYS55 4.2 10.4 1.0 CG A:PRO79 4.3 14.1 1.0 O A:LYS55 4.4 11.9 1.0 O A:PHE53 4.7 11.8 1.0 C A:LYS55 4.8 10.8 1.0 O B:HOH272 4.8 36.7 1.0 N A:ILE54 4.9 10.1 1.0

Chlorine binding site 4 out of 4 in the Hiv-1 Protease (D25N, Inactive) in Complex with Phage Display Optimized Substrate Sgiflets


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Hiv-1 Protease (D25N, Inactive) in Complex with Phage Display Optimized Substrate Sgiflets within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl101 b:13.8 occ:1.00 O B:HOH229 3.1 14.4 1.0 N B:THR74 3.2 9.1 1.0 ND2 B:ASN88 3.3 10.1 1.0 O B:HOH323 3.3 29.7 1.0 OG1 B:THR74 3.7 11.9 1.0 CB B:THR74 3.8 10.2 1.0 CA B:GLY73 3.9 9.9 1.0 CB B:ASN88 3.9 9.9 1.0 C B:GLY73 4.0 8.6 1.0 CA B:THR74 4.1 9.1 1.0 CG B:ASN88 4.1 8.8 1.0 O B:HOH257 4.1 14.2 1.0 NE2 B:GLN92 4.5 10.6 1.0 CD2 B:LEU89 4.6 13.1 1.0 O B:ASN88 4.6 10.8 1.0 O B:HOH271 4.7 35.5 1.0 O B:THR74 4.7 8.8 1.0 C B:ASN88 4.9 9.2 1.0 CA B:ASN88 4.9 9.0 1.0 C B:THR74 4.9 8.5 1.0 O B:HOH212 5.0 28.5 1.0

I.W.Windsor, R.T.Raines. A Substrate Selected By Phage Display Exhibits Enhanced Side-Chain Hydrogen Bonding to Hiv-1 Protease. Acta Crystallogr D Struct V. 74 690 2018BIOL.
ISSN: ISSN 2059-7983
PubMed: 29968678
DOI: 10.1107/S2059798318006691