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:
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
|