Calcium in PDB 8qkg: PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 125)

Enzymatic activity of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 125)

All present enzymatic activity of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 125):
3.4.21.62;

Protein crystallography data

The structure of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 125), PDB code: 8qkg 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) 30.75 / 1.54
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 53.38, 55.16, 69.03, 69.2, 78.3, 74.75
R / Rfree (%) 18 / 20.4

Calcium Binding Sites:

The binding sites of Calcium atom in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 125) (pdb code 8qkg). 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 (Mam- 125), PDB code: 8qkg:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8qkg

Go back to Calcium Binding Sites List in 8qkg
Calcium binding site 1 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 125)


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 (Mam- 125) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca702

b:15.9
occ:1.00
 OD2 A:ASP281 2.3 17.6 1.0
O A:VAL383 2.3 15.5 1.0
O A:ILE388 2.3 17.4 1.0
OD1 A:ASP325 2.4 17.6 1.0
O A:ILE390 2.4 16.3 1.0
OD1 A:ASN386 2.5 18.0 1.0
OD2 A:ASP325 2.7 18.3 1.0
CG A:ASP325 2.9 16.5 1.0
CG A:ASP281 3.4 18.9 1.0
CG A:ASN386 3.5 18.3 1.0
C A:VAL383 3.5 16.2 1.0
C A:ILE388 3.5 17.8 1.0
C A:ILE390 3.6 16.0 1.0
N A:ILE390 3.8 15.9 1.0
ND2 A:ASN386 3.8 19.8 1.0
CB A:ASP281 4.0 17.3 1.0
C A:GLY389 4.1 17.2 1.0
CA A:ILE390 4.3 16.0 1.0
CA A:GLY389 4.3 17.2 1.0
CA A:GLY384 4.3 17.0 1.0
N A:GLY389 4.4 17.6 1.0
CG1 A:ILE388 4.4 20.7 1.0
CB A:ASP325 4.4 15.9 1.0
N A:GLY384 4.4 15.9 1.0
OD1 A:ASP281 4.5 18.4 1.0
CA A:VAL383 4.5 15.0 1.0
N A:ILE388 4.5 20.3 1.0
N A:VAL383 4.5 14.5 1.0
CA A:ILE388 4.6 19.4 1.0
N A:VAL391 4.7 16.1 1.0
O A:GLY389 4.7 17.9 1.0
N A:ASN386 4.7 19.0 1.0
CB A:VAL383 4.8 16.6 1.0
CB A:ASN386 4.8 18.0 1.0
C A:GLY384 4.8 17.4 1.0
CA A:VAL391 4.9 16.9 1.0
C A:ALA382 5.0 14.9 1.0
N A:ASN385 5.0 18.0 1.0

Calcium binding site 2 out of 6 in 8qkg

Go back to Calcium Binding Sites List in 8qkg
Calcium binding site 2 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 125)


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 (Mam- 125) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca703

b:17.9
occ:1.00
 OE2 A:GLU336 2.3 18.4 1.0
OD1 A:ASP353 2.3 16.6 1.0
OD1 A:ASP346 2.3 21.1 1.0
O A:VAL350 2.3 18.2 1.0
OD1 A:ASP344 2.3 19.9 1.0
OD1 A:ASN348 2.4 20.3 1.0
CG A:ASN348 3.2 19.9 1.0
CD A:GLU336 3.3 19.0 1.0
CG A:ASP344 3.4 22.9 1.0
CG A:ASP353 3.4 16.9 1.0
CG A:ASP346 3.5 21.4 1.0
C A:VAL350 3.5 18.0 1.0
CG A:GLU336 3.7 19.1 1.0
ND2 A:ASN348 3.7 17.0 1.0
OD2 A:ASP346 3.9 21.4 1.0
OD2 A:ASP353 3.9 16.7 1.0
CA A:ASP344 4.0 20.8 1.0
OD2 A:ASP344 4.2 25.2 1.0
N A:VAL350 4.2 20.6 1.0
CB A:ASP344 4.2 20.6 1.0
CA A:VAL350 4.3 18.9 1.0
N A:ASN348 4.3 21.6 1.0
C A:ASP344 4.3 22.0 1.0
N A:ASP346 4.4 21.0 1.0
OE1 A:GLU336 4.4 18.6 1.0
CB A:ASN348 4.4 19.3 1.0
CB A:VAL350 4.5 19.3 1.0
N A:ASP345 4.5 21.1 1.0
ND2 A:ASN333 4.5 20.0 1.0
N A:ASP353 4.5 16.1 1.0
N A:VAL351 4.5 17.9 1.0
N A:ASP352 4.6 17.0 1.0
CB A:ASP353 4.6 15.0 1.0
CA A:VAL351 4.7 17.8 1.0
CB A:ASP346 4.7 20.9 1.0
CA A:ASN348 4.8 20.8 1.0
N A:SER347 4.8 22.4 1.0
C A:VAL351 4.9 17.8 1.0
CA A:ASP346 4.9 21.5 1.0
O A:ASP344 5.0 23.3 1.0

Calcium binding site 3 out of 6 in 8qkg

Go back to Calcium Binding Sites List in 8qkg
Calcium binding site 3 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 125)


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 (Mam- 125) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca704

b:19.3
occ:1.00
 OD1 A:ASP345 2.2 24.2 1.0
OD1 A:ASP352 2.3 18.2 1.0
O A:ARG340 2.3 21.3 1.0
OE1 A:GLU336 2.3 18.6 1.0
O A:HOH844 2.3 23.4 1.0
O A:VAL343 2.3 21.2 1.0
C A:ARG340 3.4 21.8 1.0
CG A:ASP345 3.5 24.9 1.0
CD A:GLU336 3.5 19.0 1.0
C A:VAL343 3.5 21.6 1.0
CG A:ASP352 3.5 19.8 1.0
N A:ARG340 3.8 22.4 1.0
N A:VAL343 3.9 21.7 1.0
CA A:ASP352 4.0 15.7 1.0
OE2 A:GLU336 4.0 18.4 1.0
N A:ASP352 4.0 17.0 1.0
CA A:VAL343 4.1 21.9 1.0
OD2 A:ASP345 4.1 26.7 1.0
CA A:ARG340 4.2 22.0 1.0
N A:ASP345 4.3 21.1 1.0
N A:LYS341 4.3 21.9 1.0
C A:GLY339 4.3 22.8 1.0
CB A:ASP352 4.3 17.1 1.0
OD2 A:ASP352 4.4 20.9 1.0
CB A:VAL343 4.4 23.2 1.0
CA A:LYS341 4.5 23.4 1.0
CB A:ASP345 4.5 21.1 1.0
O A:GLU336 4.5 18.7 1.0
N A:ASP344 4.6 21.5 1.0
N A:GLY342 4.6 23.1 1.0
CA A:GLY339 4.7 22.7 1.0
CA A:GLU336 4.7 18.1 1.0
CG A:GLU336 4.7 19.1 1.0
C A:LYS341 4.7 23.3 1.0
CB A:GLU336 4.8 18.5 1.0
CA A:ASP344 4.8 20.8 1.0
O A:GLY339 4.9 23.4 1.0
CB A:ARG340 5.0 23.4 1.0

Calcium binding site 4 out of 6 in 8qkg

Go back to Calcium Binding Sites List in 8qkg
Calcium binding site 4 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 125)


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 (Mam- 125) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca901

b:15.7
occ:1.00
 O B:VAL383 2.3 16.7 1.0
OD2 B:ASP281 2.3 16.8 1.0
OD1 B:ASP325 2.4 16.8 1.0
O B:ILE388 2.4 16.1 1.0
O B:ILE390 2.4 15.8 1.0
OD1 B:ASN386 2.5 16.5 1.0
OD2 B:ASP325 2.6 16.8 1.0
CG B:ASP325 2.8 15.6 1.0
CG B:ASP281 3.5 17.1 1.0
CG B:ASN386 3.5 18.2 1.0
C B:VAL383 3.5 16.6 1.0
C B:ILE390 3.6 15.9 1.0
C B:ILE388 3.6 16.9 1.0
N B:ILE390 3.7 15.5 1.0
ND2 B:ASN386 3.8 19.1 1.0
CB B:ASP281 4.0 16.9 1.0
C B:GLY389 4.1 16.6 1.0
CA B:ILE390 4.3 15.3 1.0
CA B:GLY389 4.3 17.3 1.0
CA B:GLY384 4.3 18.1 1.0
CB B:ASP325 4.4 16.8 1.0
N B:GLY389 4.4 17.1 1.0
N B:GLY384 4.4 17.0 1.0
CG1 B:ILE388 4.4 19.9 1.0
CA B:VAL383 4.5 15.2 1.0
OD1 B:ASP281 4.5 18.4 1.0
N B:VAL383 4.5 14.9 1.0
N B:ILE388 4.6 18.2 1.0
CA B:ILE388 4.6 17.8 1.0
N B:VAL391 4.6 15.8 1.0
O B:GLY389 4.7 17.0 1.0
N B:ASN386 4.8 18.4 1.0
CB B:VAL383 4.8 16.9 1.0
CB B:ASN386 4.8 17.5 1.0
C B:GLY384 4.9 18.8 1.0
CA B:VAL391 4.9 15.4 1.0
C B:ALA382 5.0 15.5 1.0

Calcium binding site 5 out of 6 in 8qkg

Go back to Calcium Binding Sites List in 8qkg
Calcium binding site 5 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 125)


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 (Mam- 125) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:18.7
occ:1.00
 OD1 B:ASP352 2.3 19.8 1.0
OD1 B:ASP345 2.3 24.4 1.0
OE1 B:GLU336 2.3 18.3 1.0
O B:HOH1026 2.3 20.9 1.0
O B:ARG340 2.3 19.9 1.0
O B:VAL343 2.3 22.1 1.0
C B:ARG340 3.4 20.3 1.0
CD B:GLU336 3.4 20.9 1.0
CG B:ASP345 3.5 24.2 1.0
C B:VAL343 3.5 21.9 1.0
CG B:ASP352 3.5 21.6 1.0
N B:ARG340 3.9 20.6 1.0
N B:VAL343 3.9 22.7 1.0
OE2 B:GLU336 4.0 17.4 1.0
CA B:ASP352 4.0 17.5 1.0
N B:ASP352 4.0 17.6 1.0
CA B:VAL343 4.1 22.7 1.0
OD2 B:ASP345 4.1 24.7 1.0
CA B:ARG340 4.2 20.7 1.0
N B:ASP345 4.3 21.1 1.0
N B:LYS341 4.3 20.1 1.0
CB B:ASP352 4.3 18.6 1.0
C B:GLY339 4.4 20.9 1.0
OD2 B:ASP352 4.4 22.5 1.0
CB B:VAL343 4.4 23.9 1.0
O B:GLU336 4.4 18.6 1.0
CA B:LYS341 4.5 20.5 1.0
CB B:ASP345 4.5 23.5 1.0
N B:ASP344 4.6 21.4 1.0
CA B:GLU336 4.6 17.2 1.0
CG B:GLU336 4.6 18.3 1.0
N B:GLY342 4.7 21.8 1.0
CB B:GLU336 4.7 18.5 1.0
C B:LYS341 4.7 21.6 1.0
CA B:GLY339 4.7 20.9 1.0
CA B:ASP344 4.8 21.3 1.0
O B:GLY339 5.0 20.8 1.0
CB B:ARG340 5.0 22.6 1.0

Calcium binding site 6 out of 6 in 8qkg

Go back to Calcium Binding Sites List in 8qkg
Calcium binding site 6 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 125)


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 (Mam- 125) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca903

b:19.6
occ:1.00
 OE2 B:GLU336 2.3 17.4 1.0
OD1 B:ASP344 2.3 21.6 1.0
O B:VAL350 2.3 21.6 1.0
OD1 B:ASP346 2.3 22.4 1.0
OD1 B:ASP353 2.4 18.6 1.0
OD1 B:ASN348 2.4 21.3 1.0
CG B:ASN348 3.3 21.5 1.0
CD B:GLU336 3.3 20.9 1.0
CG B:ASP344 3.3 24.5 1.0
CG B:ASP346 3.5 22.7 1.0
CG B:ASP353 3.5 18.3 1.0
C B:VAL350 3.5 21.6 1.0
CG B:GLU336 3.7 18.3 1.0
ND2 B:ASN348 3.7 20.0 1.0
OD2 B:ASP346 3.9 24.5 1.0
OD2 B:ASP353 4.0 20.3 1.0
CA B:ASP344 4.0 21.3 1.0
CB B:ASP344 4.1 22.0 1.0
N B:VAL350 4.1 24.4 1.0
OD2 B:ASP344 4.2 26.8 1.0
CA B:VAL350 4.2 22.8 1.0
N B:ASN348 4.3 25.3 1.0
C B:ASP344 4.3 22.3 1.0
N B:ASP346 4.4 23.7 1.0
OE1 B:GLU336 4.4 18.3 1.0
CB B:VAL350 4.4 23.4 1.0
N B:ASP345 4.5 21.1 1.0
CB B:ASN348 4.5 23.1 1.0
N B:VAL351 4.5 20.9 1.0
N B:ASP353 4.6 16.9 1.0
ND2 B:ASN333 4.6 18.8 1.0
N B:ASP352 4.6 17.6 1.0
CB B:ASP353 4.7 16.8 1.0
CA B:VAL351 4.7 20.2 1.0
CB B:ASP346 4.7 22.1 1.0
CA B:ASN348 4.8 24.0 1.0
N B:SER347 4.8 25.6 1.0
CA B:ASP346 4.9 23.8 1.0
C B:VAL351 4.9 19.6 1.0
O B:ASP344 4.9 23.9 1.0
C B:ASP346 5.0 25.2 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 11:17:06 2024

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