Calcium in PDB 8qke: PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13)

Enzymatic activity of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13)

All present enzymatic activity of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13):
3.4.21.62;

Protein crystallography data

The structure of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13), PDB code: 8qke was solved by F.A.Batista, M.Martinez, A.Bouillon, A.Mechaly, P.M.Alzari, A.Haouz, J.C.Barale, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 21.65 / 1.50
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 53.02, 54.71, 69.14, 69.39, 78.52, 75.02
R / Rfree (%) 20.9 / 22.6

Calcium Binding Sites:

The binding sites of Calcium atom in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13) (pdb code 8qke). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13), PDB code: 8qke:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8qke

Go back to Calcium Binding Sites List in 8qke
Calcium binding site 1 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:22.2
occ:1.00
 OD2 A:ASP281 2.3 24.4 1.0
O A:VAL383 2.3 23.9 1.0
O A:ILE388 2.3 23.5 1.0
OD1 A:ASP325 2.4 22.9 1.0
O A:ILE390 2.4 22.0 1.0
OD1 A:ASN386 2.5 22.2 1.0
OD2 A:ASP325 2.7 21.5 1.0
CG A:ASP325 2.9 21.2 1.0
CG A:ASP281 3.4 25.6 1.0
CG A:ASN386 3.5 23.8 1.0
C A:VAL383 3.5 23.0 1.0
C A:ILE388 3.5 23.7 1.0
C A:ILE390 3.6 21.8 1.0
N A:ILE390 3.8 21.2 1.0
ND2 A:ASN386 3.8 25.0 1.0
CB A:ASP281 4.0 23.9 1.0
C A:GLY389 4.0 22.1 1.0
CA A:ILE390 4.3 21.5 1.0
CA A:GLY389 4.3 22.6 1.0
CA A:GLY384 4.3 22.8 1.0
N A:GLY384 4.4 21.9 1.0
N A:GLY389 4.4 22.4 1.0
CB A:ASP325 4.4 21.1 1.0
CG1 A:ILE388 4.4 25.2 1.0
CA A:VAL383 4.4 21.4 1.0
OD1 A:ASP281 4.4 24.7 1.0
N A:VAL383 4.5 21.1 1.0
N A:ILE388 4.5 24.5 1.0
CA A:ILE388 4.5 23.8 1.0
O A:GLY389 4.6 22.9 1.0
N A:VAL391 4.6 21.3 1.0
N A:ASN386 4.7 24.1 1.0
CB A:VAL383 4.8 23.2 1.0
CB A:ASN386 4.8 23.9 1.0
C A:GLY384 4.8 24.0 1.0
CA A:VAL391 4.9 21.5 1.0
C A:ALA382 4.9 21.6 1.0
N A:ASN385 5.0 23.6 1.0

Calcium binding site 2 out of 6 in 8qke

Go back to Calcium Binding Sites List in 8qke
Calcium binding site 2 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:28.4
occ:1.00
 O A:VAL350 2.2 28.3 1.0
OD1 A:ASP344 2.3 35.2 1.0
OD1 A:ASP353 2.3 24.2 1.0
OE2 A:GLU336 2.3 29.5 1.0
OD1 A:ASP346 2.4 31.7 1.0
OD1 A:ASN348 2.4 34.0 1.0
CG A:ASN348 3.3 33.6 1.0
CD A:GLU336 3.4 29.0 1.0
CG A:ASP344 3.4 36.9 1.0
C A:VAL350 3.4 28.8 1.0
CG A:ASP353 3.5 25.0 1.0
CG A:ASP346 3.5 32.4 1.0
CG A:GLU336 3.7 28.6 1.0
ND2 A:ASN348 3.8 31.4 1.0
OD2 A:ASP346 4.0 31.7 1.0
OD2 A:ASP353 4.0 25.4 1.0
N A:VAL350 4.0 32.5 1.0
CA A:ASP344 4.1 33.0 1.0
CA A:VAL350 4.2 30.6 1.0
CB A:ASP344 4.2 33.7 1.0
OD2 A:ASP344 4.2 40.7 1.0
N A:ASN348 4.2 37.5 1.0
CB A:VAL350 4.4 31.5 1.0
ND2 A:ASN333 4.4 26.4 1.0
CB A:ASN348 4.4 35.1 1.0
C A:ASP344 4.5 34.0 1.0
N A:VAL351 4.5 27.8 1.0
OE1 A:GLU336 4.5 24.8 1.0
N A:ASP346 4.5 35.4 1.0
N A:ASP353 4.5 22.7 1.0
N A:ASP352 4.6 24.5 1.0
CB A:ASP353 4.6 22.9 1.0
CA A:VAL351 4.6 27.7 1.0
CA A:ASN348 4.7 36.1 1.0
N A:ASP345 4.7 33.7 1.0
CB A:ASP346 4.7 34.4 1.0
N A:SER347 4.8 37.9 1.0
C A:VAL351 4.9 26.2 1.0
N A:GLY349 4.9 36.2 1.0
C A:ASN348 4.9 36.6 1.0
CA A:ASP346 5.0 35.5 1.0

Calcium binding site 3 out of 6 in 8qke

Go back to Calcium Binding Sites List in 8qke
Calcium binding site 3 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:30.4
occ:1.00
 O A:VAL343 2.2 34.1 1.0
OD1 A:ASP352 2.3 27.4 1.0
OD1 A:ASP345 2.3 36.0 1.0
OE1 A:GLU336 2.4 24.8 1.0
O A:ARG340 2.5 31.9 1.0
C A:VAL343 3.4 33.7 1.0
C A:ARG340 3.5 33.5 1.0
CG A:ASP352 3.5 28.2 1.0
CG A:ASP345 3.5 37.3 1.0
CD A:GLU336 3.5 29.0 1.0
N A:VAL343 3.9 34.0 1.0
N A:ARG340 3.9 33.1 1.0
CA A:ASP352 4.0 23.2 1.0
N A:ASP352 4.0 24.5 1.0
CA A:VAL343 4.0 34.2 1.0
OE2 A:GLU336 4.1 29.5 1.0
OD2 A:ASP345 4.2 38.8 1.0
CB A:VAL343 4.3 35.6 1.0
N A:ASP345 4.3 33.7 1.0
CB A:ASP352 4.3 24.3 1.0
CA A:ARG340 4.3 34.0 1.0
C A:GLY339 4.4 32.9 1.0
N A:LYS341 4.4 34.1 1.0
O A:GLU336 4.4 26.2 1.0
OD2 A:ASP352 4.4 28.7 1.0
N A:ASP344 4.5 32.7 1.0
CA A:LYS341 4.5 35.6 1.0
CB A:ASP345 4.5 34.9 1.0
CA A:GLU336 4.6 26.0 1.0
CA A:GLY339 4.6 32.3 1.0
N A:GLY342 4.7 34.3 1.0
C A:LYS341 4.7 35.2 1.0
CG A:GLU336 4.7 28.6 1.0
CA A:ASP344 4.8 33.0 1.0
CB A:GLU336 4.8 26.2 1.0

Calcium binding site 4 out of 6 in 8qke

Go back to Calcium Binding Sites List in 8qke
Calcium binding site 4 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca901

b:24.5
occ:1.00
 OD2 B:ASP281 2.3 27.1 1.0
O B:VAL383 2.3 25.7 1.0
O B:ILE388 2.3 25.4 1.0
O B:ILE390 2.4 24.6 1.0
OD1 B:ASP325 2.4 25.0 1.0
OD1 B:ASN386 2.5 26.1 1.0
OD2 B:ASP325 2.6 24.6 1.0
CG B:ASP325 2.9 23.4 1.0
CG B:ASP281 3.4 28.5 1.0
CG B:ASN386 3.5 27.4 1.0
C B:VAL383 3.5 26.1 1.0
C B:ILE388 3.5 25.8 1.0
C B:ILE390 3.5 24.5 1.0
N B:ILE390 3.7 23.0 1.0
ND2 B:ASN386 3.8 28.5 1.0
C B:GLY389 4.0 24.0 1.0
CB B:ASP281 4.0 27.5 1.0
CA B:ILE390 4.2 23.5 1.0
CA B:GLY389 4.3 24.3 1.0
N B:GLY389 4.4 24.3 1.0
CA B:GLY384 4.4 27.4 1.0
CB B:ASP325 4.4 24.3 1.0
N B:GLY384 4.4 26.5 1.0
CG1 B:ILE388 4.4 29.1 1.0
OD1 B:ASP281 4.4 28.8 1.0
CA B:VAL383 4.5 24.8 1.0
N B:ILE388 4.5 27.2 1.0
N B:VAL383 4.5 23.6 1.0
CA B:ILE388 4.5 26.8 1.0
N B:VAL391 4.6 24.2 1.0
O B:GLY389 4.6 24.6 1.0
N B:ASN386 4.8 28.3 1.0
CB B:VAL383 4.8 26.1 1.0
CB B:ASN386 4.8 27.0 1.0
C B:GLY384 4.9 28.1 1.0
CA B:VAL391 4.9 23.6 1.0
C B:ALA382 4.9 23.7 1.0
N B:ASN385 5.0 28.4 1.0

Calcium binding site 5 out of 6 in 8qke

Go back to Calcium Binding Sites List in 8qke
Calcium binding site 5 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:26.4
occ:1.00
 OD1 B:ASP345 2.2 37.2 1.0
OD1 B:ASP352 2.3 30.2 1.0
O B:VAL343 2.3 32.1 1.0
OE1 B:GLU336 2.4 26.3 1.0
O B:ARG340 2.4 27.3 1.0
O B:HOH1005 2.4 27.9 1.0
CG B:ASP345 3.4 37.8 1.0
C B:ARG340 3.4 28.6 1.0
C B:VAL343 3.5 32.9 1.0
CD B:GLU336 3.5 28.4 1.0
CG B:ASP352 3.5 31.8 1.0
N B:ARG340 3.9 30.7 1.0
N B:VAL343 3.9 32.5 1.0
OD2 B:ASP345 4.0 39.2 1.0
CA B:ASP352 4.0 28.4 1.0
N B:ASP352 4.1 28.9 1.0
OE2 B:GLU336 4.1 25.5 1.0
CA B:VAL343 4.1 33.0 1.0
CA B:ARG340 4.2 30.4 1.0
N B:ASP345 4.3 34.1 1.0
N B:LYS341 4.3 28.7 1.0
CB B:VAL343 4.3 34.5 1.0
O B:GLU336 4.4 27.0 1.0
CB B:ASP352 4.4 29.8 1.0
C B:GLY339 4.4 30.5 1.0
OD2 B:ASP352 4.4 32.2 1.0
CA B:LYS341 4.4 30.0 1.0
CB B:ASP345 4.5 35.3 1.0
N B:ASP344 4.6 32.8 1.0
CA B:GLU336 4.6 26.4 1.0
N B:GLY342 4.7 31.5 1.0
CG B:GLU336 4.7 28.1 1.0
C B:LYS341 4.7 31.2 1.0
CB B:GLU336 4.7 27.0 1.0
CA B:GLY339 4.7 30.3 1.0
CA B:ASP344 4.8 33.5 1.0
C B:GLU336 5.0 26.7 1.0
O B:GLY339 5.0 30.0 1.0

Calcium binding site 6 out of 6 in 8qke

Go back to Calcium Binding Sites List in 8qke
Calcium binding site 6 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mh- 13) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca903

b:29.6
occ:1.00
 OD1 B:ASP346 2.2 34.5 1.0
OE2 B:GLU336 2.2 25.5 1.0
O B:VAL350 2.3 32.5 1.0
OD1 B:ASP353 2.3 28.2 1.0
OD1 B:ASN348 2.4 34.4 1.0
OD1 B:ASP344 2.4 35.6 1.0
CG B:ASN348 3.3 36.7 1.0
CD B:GLU336 3.3 28.4 1.0
CG B:ASP346 3.3 36.2 1.0
CG B:ASP344 3.4 37.2 1.0
CG B:ASP353 3.4 29.3 1.0
C B:VAL350 3.5 32.2 1.0
ND2 B:ASN348 3.7 35.6 1.0
CG B:GLU336 3.7 28.1 1.0
OD2 B:ASP346 3.8 37.0 1.0
OD2 B:ASP353 3.9 29.6 1.0
CA B:ASP344 4.0 33.5 1.0
N B:VAL350 4.1 35.7 1.0
CB B:ASP344 4.2 34.0 1.0
CA B:VAL350 4.2 33.7 1.0
OD2 B:ASP344 4.3 39.4 1.0
N B:ASN348 4.3 39.9 1.0
N B:ASP346 4.3 37.0 1.0
C B:ASP344 4.3 34.7 1.0
OE1 B:GLU336 4.4 26.3 1.0
CB B:VAL350 4.4 33.5 1.0
ND2 B:ASN333 4.4 32.3 1.0
CB B:ASN348 4.5 37.6 1.0
N B:ASP345 4.5 34.1 1.0
N B:VAL351 4.5 31.1 1.0
N B:ASP353 4.6 26.7 1.0
CB B:ASP346 4.6 37.0 1.0
CB B:ASP353 4.6 26.8 1.0
N B:ASP352 4.7 28.9 1.0
CA B:VAL351 4.7 30.4 1.0
N B:SER347 4.8 40.4 1.0
CA B:ASP346 4.8 37.8 1.0
CA B:ASN348 4.8 38.6 1.0
C B:ASP346 4.9 39.8 1.0
C B:VAL351 4.9 30.2 1.0
O B:ASP344 5.0 36.0 1.0

Reference:

A.Legru, F.A.Batista, A.K.Puszkoa, A.Bouillon, M.Maurel, M.Martinez, A.Ejjoummanya, L.Ortega Varga, P.Adler, A.Mechaly, M.Hadjadj, P.Sosnowski, G.Hopfgartner, P.M.Alzari, A.Blondel, A.Haouz, J.C.Barale, J.F.Hernandez. Insights From Structure-Activity Relationships and the Binding Mode of Peptidic Alpha-Ketoamide Inhibitors of the Malaria Drug Target Subtilisin-Like SUB1 To Be Published.
Page generated: Fri Jul 19 11:17:05 2024

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