Chlorine in PDB 4dku: Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-09027

The structure of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-09027, PDB code: 4dku was solved by Y.D.Kwon, A.K.Debnath, P.D.Kwong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.50 / 2.49
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	64.232, 68.436, 93.967, 90.00, 91.81, 90.00
R / Rfree (%)	20 / 24.9

The binding sites of Chlorine atom in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-09027 (pdb code 4dku). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-09027, PDB code: 4dku:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-09027


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-09027 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl512 b:88.3 occ:1.00 CL1 A:0KU512 0.0 88.3 1.0 C01 A:0KU512 1.7 58.5 1.0 C06 A:0KU512 2.6 50.6 1.0 C02 A:0KU512 2.7 59.0 1.0 H4 A:0KU512 2.7 60.7 1.0 H1 A:0KU512 2.8 70.8 1.0 CA A:PHE376 3.5 37.6 1.0 C A:PHE376 3.6 43.5 1.0 N A:PHE376 3.7 38.0 1.0 CD2 A:PHE382 3.8 57.6 1.0 C05 A:0KU512 3.9 65.1 1.0 C03 A:0KU512 3.9 59.0 1.0 N A:ASN377 4.0 37.2 1.0 C A:SER375 4.0 44.6 1.0 O A:PHE376 4.0 39.1 1.0 O A:VAL255 4.1 41.6 1.0 CE2 A:PHE382 4.1 54.6 1.0 CG1 A:VAL255 4.1 29.2 1.0 O A:SER375 4.1 46.1 1.0 OG A:SER375 4.3 56.6 1.0 C04 A:0KU512 4.4 67.0 1.0 CB A:SER375 4.5 42.5 1.0 CB A:ASN377 4.6 44.0 1.0 H3 A:0KU512 4.7 78.1 1.0 C A:VAL255 4.7 34.7 1.0 H2 A:0KU512 4.7 70.8 1.0 CA A:ASN377 4.8 38.6 1.0 CA A:SER375 4.9 38.9 1.0 CB A:VAL255 4.9 33.5 1.0 CA A:SER256 4.9 34.4 1.0 CB A:PHE376 5.0 33.9 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-09027


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Clade A/E 93TH057 Hiv-1 GP120 Core in Complex with Nbd-09027 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl511 b:1.0 occ:1.00 CL1 B:0KU511 0.0 1.0 1.0 C01 B:0KU511 1.7 72.8 1.0 C06 B:0KU511 2.6 75.7 1.0 C02 B:0KU511 2.7 71.2 1.0 H4 B:0KU511 2.7 90.8 1.0 H1 B:0KU511 2.8 85.4 1.0 O B:VAL255 3.8 52.2 1.0 CA B:PHE376 3.8 39.9 1.0 N B:PHE376 3.9 47.6 1.0 C05 B:0KU511 3.9 67.8 1.0 C03 B:0KU511 3.9 70.8 1.0 C B:PHE376 4.1 51.8 1.0 CG1 B:VAL255 4.1 41.6 1.0 C B:SER375 4.1 47.7 1.0 O B:SER375 4.3 40.8 1.0 OG B:SER375 4.3 60.5 1.0 CD1 B:PHE382 4.3 54.5 1.0 N B:ASN377 4.3 53.9 1.0 CB B:SER375 4.4 56.9 1.0 C04 B:0KU511 4.4 75.6 1.0 C B:VAL255 4.5 56.5 1.0 O B:PHE376 4.6 51.0 1.0 CH2 B:TRP112 4.6 43.3 1.0 CE1 B:PHE382 4.7 49.7 1.0 H3 B:0KU511 4.7 81.4 1.0 H2 B:0KU511 4.7 84.9 1.0 CB B:VAL255 4.8 39.9 1.0 CA B:SER256 4.9 45.7 1.0 CA B:SER375 4.9 52.5 1.0

F.Curreli, Y.D.Kwon, H.Zhang, Y.Yang, D.Scacalossi, P.D.Kwong, A.K.Debnath. Binding Mode Characterization of Nbd Series CD4-Mimetic Hiv-1 Entry Inhibitors By X-Ray Structure and Resistance Study. Antimicrob. Agents V. 58 5478 2014CHEMOTHER..
ISSN: ESSN 1098-6596
PubMed: 25001301
DOI: 10.1128/AAC.03339-14