Atomistry » Yttrium » PDB 3ph6-8pun » 6prf
Atomistry »
  Yttrium »
    PDB 3ph6-8pun »
      6prf »

Yttrium in PDB 6prf: Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A

Enzymatic activity of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A

All present enzymatic activity of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A:
3.4.23.16;

Protein crystallography data

The structure of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A, PDB code: 6prf was solved by D.W.Kneller, J.Agniswamy, I.T.Weber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.55 / 1.21
Space group P 61
Cell size a, b, c (Å), α, β, γ (°) 60.565, 60.565, 85.139, 90.00, 90.00, 120.00
R / Rfree (%) 15.2 / 19

Other elements in 6prf:

The structure of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A also contains other interesting chemical elements:

Fluorine (F) 4 atoms

Yttrium Binding Sites:

The binding sites of Yttrium atom in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A (pdb code 6prf). This binding sites where shown within 5.0 Angstroms radius around Yttrium atom.
In total 9 binding sites of Yttrium where determined in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A, PDB code: 6prf:
Jump to Yttrium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Yttrium binding site 1 out of 9 in 6prf

Go back to Yttrium Binding Sites List in 6prf
Yttrium binding site 1 out of 9 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 1 of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y101

b:18.6
occ:0.20
 Y A:Y1103 1.1 22.2 0.2
Y A:Y1102 1.5 15.3 0.2
OE1 A:GLU58 2.1 39.4 1.0
O A:HOH257 2.4 19.9 0.3
O A:HOH207 2.4 12.9 0.3
O A:HOH271 2.5 21.3 0.2
O A:HOH278 2.6 19.4 0.3
OD1 A:ASP60 2.6 33.1 1.0
OD2 A:ASP60 3.2 33.4 1.0
CG A:ASP60 3.2 37.0 1.0
CD A:GLU58 3.2 32.3 1.0
O A:HOH247 3.8 20.8 0.3
OE2 A:GLU58 4.1 49.1 1.0
CG A:GLU58 4.1 19.5 1.0
CB A:ASP60 4.7 28.6 1.0
OG1 A:THR74 4.8 27.0 1.0
CG2 A:THR74 5.0 19.7 1.0

Yttrium binding site 2 out of 9 in 6prf

Go back to Yttrium Binding Sites List in 6prf
Yttrium binding site 2 out of 9 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 2 of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y102

b:15.3
occ:0.20
 O A:HOH257 1.0 19.9 0.3
Y A:Y1101 1.5 18.6 0.2
O A:HOH207 1.8 12.9 0.3
O A:HOH271 2.3 21.3 0.2
O A:HOH278 2.4 19.4 0.3
OD2 A:ASP60 2.5 33.4 1.0
O A:HOH247 2.5 20.8 0.3
Y A:Y1103 2.6 22.2 0.2
OD1 A:ASP60 2.7 33.1 1.0
OE1 A:GLU58 2.8 39.4 1.0
CG A:ASP60 2.9 37.0 1.0
CD A:GLU58 3.9 32.3 1.0
CG A:GLU58 4.4 19.5 1.0
CB A:ASP60 4.4 28.6 1.0
O A:HOH295 4.5 32.1 1.0
CD A:LYS43 4.7 25.5 0.5
CG A:LYS43 4.7 35.9 0.5
CG A:LYS43 4.8 26.8 0.5
CB A:LYS43 4.9 30.2 0.5
OE2 A:GLU58 4.9 49.1 1.0

Yttrium binding site 3 out of 9 in 6prf

Go back to Yttrium Binding Sites List in 6prf
Yttrium binding site 3 out of 9 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 3 of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y103

b:22.2
occ:0.20
 Y A:Y1101 1.1 18.6 0.2
OE1 A:GLU58 2.2 39.4 1.0
Y A:Y1102 2.6 15.3 0.2
OD1 A:ASP60 2.9 33.1 1.0
O A:HOH278 3.1 19.4 0.3
O A:HOH271 3.1 21.3 0.2
O A:HOH207 3.1 12.9 0.3
CD A:GLU58 3.2 32.3 1.0
O A:HOH257 3.4 19.9 0.3
CG A:ASP60 3.7 37.0 1.0
OE2 A:GLU58 3.8 49.1 1.0
OD2 A:ASP60 3.9 33.4 1.0
OG1 A:THR74 4.3 27.0 1.0
CG A:GLU58 4.3 19.5 1.0
O A:HOH281 4.5 39.2 1.0
CG2 A:THR74 4.6 19.7 1.0
O A:HOH247 4.7 20.8 0.3

Yttrium binding site 4 out of 9 in 6prf

Go back to Yttrium Binding Sites List in 6prf
Yttrium binding site 4 out of 9 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 4 of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Y104

b:28.6
occ:0.35
 O A:HOH287 1.4 20.7 0.2
C A:GLY78 3.3 15.6 1.0
CG A:GLU34 3.3 27.7 1.0
N A:ASP35 3.5 21.1 1.0
O A:HOH251 3.5 41.0 1.0
N A:PRO79 3.6 17.7 1.0
CA A:GLY78 3.6 15.8 1.0
O A:GLY78 3.6 16.0 1.0
CA A:GLU34 3.9 14.3 1.0
CA A:PRO79 3.9 17.7 1.0
CD A:PRO79 4.0 19.4 1.0
N A:GLY78 4.0 13.7 1.0
CB A:GLU34 4.2 17.9 1.0
OE2 A:GLU34 4.2 40.5 1.0
C A:GLU34 4.3 15.6 1.0
CB A:PRO79 4.3 22.0 1.0
CD A:GLU34 4.3 34.7 1.0
OD1 A:ASP35 4.3 39.0 1.0
CG1 A:VAL77 4.4 13.6 0.5
CA A:ASP35 4.5 25.4 1.0
CG1 A:VAL77 4.6 15.0 0.5
O A:HOH228 4.7 35.1 1.0
CG A:PRO79 4.8 19.8 1.0
C A:VAL77 4.8 13.1 1.0
O A:PHE33 4.9 12.5 0.7
O A:PHE33 5.0 13.2 0.3
CG A:ASP35 5.0 39.6 1.0

Yttrium binding site 5 out of 9 in 6prf

Go back to Yttrium Binding Sites List in 6prf
Yttrium binding site 5 out of 9 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 5 of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y102

b:74.1
occ:0.20
 Y B:Y1105 2.1 21.2 0.2
OE2 B:GLU58 2.6 35.2 1.0
O B:HOH279 2.9 24.2 0.5
Y B:Y1103 3.1 20.3 0.2
NZ B:LYS45 3.6 34.1 0.5
CD B:GLU58 3.6 30.3 1.0
O B:HOH224 4.1 18.5 0.2
OE1 B:GLU58 4.1 42.9 1.0
CE B:LYS45 4.5 28.2 0.5
Y B:Y1104 4.5 17.2 0.2
NZ B:LYS45 4.7 32.8 0.5
CG B:GLU58 4.8 19.4 1.0
OD1 B:ASP60 4.8 33.5 1.0
OG1 B:THR74 4.9 28.4 1.0
CG2 B:THR74 4.9 19.3 1.0
CE B:LYS45 5.0 34.8 0.5

Yttrium binding site 6 out of 9 in 6prf

Go back to Yttrium Binding Sites List in 6prf
Yttrium binding site 6 out of 9 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 6 of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y103

b:20.3
occ:0.25
 Y B:Y1105 1.1 21.2 0.2
Y B:Y1104 1.5 17.2 0.2
OE2 B:GLU58 2.2 35.2 1.0
O B:HOH224 2.5 18.5 0.2
O B:HOH214 2.5 21.9 0.2
OD1 B:ASP60 2.6 33.5 1.0
CD B:GLU58 2.8 30.3 1.0
Y B:Y1102 3.1 74.1 0.2
OD2 B:ASP60 3.1 33.4 1.0
OE1 B:GLU58 3.1 42.9 1.0
CG B:ASP60 3.2 38.3 1.0
O B:HOH238 3.9 26.2 0.5
CG B:GLU58 4.1 19.4 1.0
CB B:ASP60 4.6 28.1 1.0
NZ B:LYS45 4.8 34.1 0.5
Y B:Y1106 4.8 27.0 0.3
OG1 B:THR74 4.8 28.4 1.0
O B:HOH294 4.9 38.5 0.5
O B:HOH215 5.0 29.0 0.5

Yttrium binding site 7 out of 9 in 6prf

Go back to Yttrium Binding Sites List in 6prf
Yttrium binding site 7 out of 9 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 7 of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y104

b:17.2
occ:0.25
 O B:HOH214 1.3 21.9 0.2
Y B:Y1103 1.5 20.3 0.2
O B:HOH224 2.2 18.5 0.2
OD2 B:ASP60 2.4 33.4 1.0
Y B:Y1105 2.6 21.2 0.2
O B:HOH238 2.7 26.2 0.5
OD1 B:ASP60 2.7 33.5 1.0
CG B:ASP60 2.9 38.3 1.0
OE1 B:GLU58 3.0 42.9 1.0
OE2 B:GLU58 3.0 35.2 1.0
CD B:GLU58 3.2 30.3 1.0
CG B:GLU58 4.3 19.4 1.0
O B:HOH215 4.4 29.0 0.5
CB B:ASP60 4.4 28.1 1.0
Y B:Y1102 4.5 74.1 0.2
O B:HOH291 4.5 33.4 1.0
Y B:Y1106 4.6 27.0 0.3
CG B:LYS43 4.7 36.0 1.0
O B:HOH294 4.8 38.5 0.5
CD B:LYS43 5.0 41.5 1.0

Yttrium binding site 8 out of 9 in 6prf

Go back to Yttrium Binding Sites List in 6prf
Yttrium binding site 8 out of 9 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 8 of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y105

b:21.2
occ:0.20
 Y B:Y1103 1.1 20.3 0.2
OE2 B:GLU58 2.0 35.2 1.0
Y B:Y1102 2.1 74.1 0.2
Y B:Y1104 2.6 17.2 0.2
OD1 B:ASP60 2.9 33.5 1.0
CD B:GLU58 3.0 30.3 1.0
O B:HOH224 3.1 18.5 0.2
O B:HOH214 3.5 21.9 0.2
OE1 B:GLU58 3.5 42.9 1.0
CG B:ASP60 3.7 38.3 1.0
OD2 B:ASP60 3.9 33.4 1.0
CG B:GLU58 4.2 19.4 1.0
OG1 B:THR74 4.3 28.4 1.0
O B:HOH279 4.4 24.2 0.5
NZ B:LYS45 4.6 34.1 0.5
CG2 B:THR74 4.6 19.3 1.0
O B:HOH238 4.9 26.2 0.5

Yttrium binding site 9 out of 9 in 6prf

Go back to Yttrium Binding Sites List in 6prf
Yttrium binding site 9 out of 9 in the Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A


Mono view


Stereo pair view

A full contact list of Yttrium with other atoms in the Y binding site number 9 of Hiv-1 Protease Multiple Drug Resistant Clinical Isolate Mutant PR20 with Grl-14213A within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Y106

b:27.0
occ:0.30
 O B:HOH215 1.4 29.0 0.5
O B:HOH294 1.5 38.5 0.5
O B:HOH224 3.1 18.5 0.2
NZ B:LYS43 3.9 41.8 1.0
CE B:LYS43 4.4 43.7 1.0
Y B:Y1104 4.6 17.2 0.2
CD B:LYS43 4.6 41.5 1.0
Y B:Y1103 4.8 20.3 0.2

Reference:

D.W.Kneller, J.Agniswamy, A.K.Ghosh, I.T.Weber. Potent Antiviral Hiv-1 Protease Inhibitor Combats Highly Drug Resistant Mutant PR20. Biochem.Biophys.Res.Commun. V. 519 61 2019.
ISSN: ESSN 1090-2104
PubMed: 31474336
DOI: 10.1016/J.BBRC.2019.08.126
Page generated: Sat Oct 12 20:49:46 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy