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Calcium in PDB 8qkj: PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 133)

Enzymatic activity of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 133)

All present enzymatic activity of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 133):
3.4.21.62;

Protein crystallography data

The structure of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 133), PDB code: 8qkj 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) 25.77 / 1.77
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 53.36, 55.13, 69.17, 68.79, 78.31, 74.92
R / Rfree (%) 18.5 / 20.2

Calcium Binding Sites:

The binding sites of Calcium atom in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 133) (pdb code 8qkj). 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- 133), PDB code: 8qkj:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 8qkj

Go back to Calcium Binding Sites List in 8qkj
Calcium binding site 1 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 133)


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- 133) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:17.7
occ:1.00
 OD2 A:ASP281 2.3 19.7 1.0
OD1 A:ASP325 2.3 16.1 1.0
O A:VAL383 2.4 17.7 1.0
O A:ILE388 2.4 19.0 1.0
O A:ILE390 2.4 18.6 1.0
OD1 A:ASN386 2.5 19.4 1.0
OD2 A:ASP325 2.7 17.1 1.0
CG A:ASP325 2.8 16.5 1.0
CG A:ASP281 3.4 19.8 1.0
CG A:ASN386 3.5 19.8 1.0
C A:VAL383 3.6 17.4 1.0
C A:ILE388 3.6 20.3 1.0
C A:ILE390 3.6 17.5 1.0
N A:ILE390 3.7 16.8 1.0
ND2 A:ASN386 3.8 20.2 1.0
C A:GLY389 4.0 18.4 1.0
CB A:ASP281 4.0 18.9 1.0
CA A:ILE390 4.3 17.0 1.0
CA A:GLY389 4.3 18.9 1.0
CB A:ASP325 4.3 14.9 1.0
N A:GLY389 4.4 19.2 1.0
OD1 A:ASP281 4.4 19.5 1.0
CA A:GLY384 4.4 18.3 1.0
N A:GLY384 4.4 16.9 1.0
CG1 A:ILE388 4.5 23.2 1.0
CA A:VAL383 4.5 16.8 1.0
N A:VAL383 4.5 15.8 1.0
N A:ILE388 4.5 22.6 1.0
CA A:ILE388 4.6 21.9 1.0
O A:GLY389 4.6 19.5 1.0
N A:VAL391 4.6 17.5 1.0
N A:ASN386 4.8 20.4 1.0
CB A:ASN386 4.8 20.2 1.0
CB A:VAL383 4.8 18.2 1.0
C A:GLY384 4.9 19.6 1.0
CA A:VAL391 4.9 17.7 1.0
C A:ALA382 4.9 15.6 1.0

Calcium binding site 2 out of 6 in 8qkj

Go back to Calcium Binding Sites List in 8qkj
Calcium binding site 2 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 133)


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- 133) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:22.3
occ:1.00
 OE2 A:GLU336 2.3 24.5 1.0
OD1 A:ASP353 2.3 18.4 1.0
O A:VAL350 2.3 25.3 1.0
OD1 A:ASP346 2.3 25.1 1.0
OD1 A:ASP344 2.4 29.9 1.0
OD1 A:ASN348 2.4 27.8 1.0
CD A:GLU336 3.3 23.1 1.0
CG A:ASN348 3.3 27.3 1.0
CG A:ASP353 3.4 18.8 1.0
CG A:ASP344 3.4 31.4 1.0
CG A:ASP346 3.4 26.1 1.0
C A:VAL350 3.5 25.7 1.0
CG A:GLU336 3.6 22.9 1.0
ND2 A:ASN348 3.7 25.5 1.0
OD2 A:ASP346 3.9 24.5 1.0
OD2 A:ASP353 3.9 19.7 1.0
CA A:ASP344 4.1 26.8 1.0
N A:VAL350 4.2 29.0 1.0
CB A:ASP344 4.2 27.1 1.0
OD2 A:ASP344 4.2 32.8 1.0
CA A:VAL350 4.2 27.3 1.0
N A:ASN348 4.4 28.6 1.0
C A:ASP344 4.4 27.9 1.0
N A:ASP346 4.4 26.9 1.0
OE1 A:GLU336 4.4 19.3 1.0
ND2 A:ASN333 4.4 20.4 1.0
CB A:VAL350 4.5 27.6 1.0
N A:ASP345 4.5 26.8 1.0
N A:VAL351 4.5 24.9 1.0
CB A:ASN348 4.5 27.4 1.0
N A:ASP353 4.5 18.0 1.0
CB A:ASP353 4.6 17.8 1.0
N A:ASP352 4.6 21.2 1.0
CA A:VAL351 4.7 23.8 1.0
CB A:ASP346 4.7 25.8 1.0
N A:SER347 4.8 28.7 1.0
CA A:ASN348 4.9 27.7 1.0
C A:VAL351 4.9 22.9 1.0
CA A:ASP346 4.9 26.9 1.0

Calcium binding site 3 out of 6 in 8qkj

Go back to Calcium Binding Sites List in 8qkj
Calcium binding site 3 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 133)


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- 133) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:24.7
occ:1.00
 OD1 A:ASP352 2.3 20.8 1.0
OD2 A:ASP345 2.3 34.3 1.0
OE1 A:GLU336 2.3 19.3 1.0
O A:VAL343 2.3 26.6 1.0
O A:ARG340 2.4 29.9 1.0
CD A:GLU336 3.4 23.1 1.0
C A:ARG340 3.4 29.5 1.0
C A:VAL343 3.5 27.0 1.0
CG A:ASP352 3.5 22.0 1.0
CG A:ASP345 3.5 32.7 1.0
N A:ARG340 3.8 28.7 1.0
N A:VAL343 3.9 27.5 1.0
CA A:ASP352 3.9 19.4 1.0
OE2 A:GLU336 4.0 24.5 1.0
N A:ASP352 4.0 21.2 1.0
CA A:VAL343 4.1 27.7 1.0
OD1 A:ASP345 4.2 33.5 1.0
CA A:ARG340 4.2 29.5 1.0
CB A:ASP352 4.3 19.9 1.0
C A:GLY339 4.3 28.0 1.0
N A:ASP345 4.3 26.8 1.0
N A:LYS341 4.4 29.2 1.0
OD2 A:ASP352 4.4 24.4 1.0
CB A:VAL343 4.4 29.0 1.0
O A:GLU336 4.5 21.4 1.0
CA A:LYS341 4.5 29.9 1.0
N A:ASP344 4.6 26.6 1.0
CB A:ASP345 4.6 28.4 1.0
CA A:GLY339 4.6 27.7 1.0
N A:GLY342 4.7 28.3 1.0
CA A:GLU336 4.7 21.0 1.0
CG A:GLU336 4.7 22.9 1.0
C A:LYS341 4.7 29.7 1.0
CB A:GLU336 4.8 20.4 1.0
CA A:ASP344 4.9 26.8 1.0
O A:GLY339 4.9 27.1 1.0

Calcium binding site 4 out of 6 in 8qkj

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Calcium binding site 4 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 133)


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

b:19.9
occ:1.00
 OD2 B:ASP281 2.3 21.3 1.0
OD1 B:ASP325 2.3 18.3 1.0
O B:VAL383 2.4 19.1 1.0
O B:ILE388 2.4 19.3 1.0
O B:ILE390 2.4 17.8 1.0
OD1 B:ASN386 2.5 20.6 1.0
OD2 B:ASP325 2.7 19.9 1.0
CG B:ASP325 2.8 18.6 1.0
CG B:ASP281 3.4 21.4 1.0
CG B:ASN386 3.5 21.5 1.0
C B:ILE390 3.6 17.9 1.0
C B:VAL383 3.6 19.1 1.0
C B:ILE388 3.6 20.1 1.0
N B:ILE390 3.7 17.3 1.0
ND2 B:ASN386 3.8 21.0 1.0
CB B:ASP281 4.0 21.6 1.0
C B:GLY389 4.0 19.6 1.0
CA B:ILE390 4.3 17.5 1.0
CB B:ASP325 4.4 18.5 1.0
CA B:GLY389 4.4 19.1 1.0
N B:GLY389 4.4 19.5 1.0
N B:GLY384 4.5 19.8 1.0
CA B:GLY384 4.5 21.3 1.0
OD1 B:ASP281 4.5 22.5 1.0
CG1 B:ILE388 4.5 23.8 1.0
CA B:VAL383 4.5 18.3 1.0
N B:VAL383 4.5 17.3 1.0
N B:ILE388 4.6 21.7 1.0
CA B:ILE388 4.6 21.3 1.0
N B:VAL391 4.6 17.8 1.0
O B:GLY389 4.6 21.4 1.0
N B:ASN386 4.8 22.8 1.0
CB B:ASN386 4.8 21.2 1.0
CB B:VAL383 4.8 19.2 1.0
CA B:VAL391 4.9 17.1 1.0
C B:GLY384 4.9 22.5 1.0
C B:ALA382 4.9 17.4 1.0

Calcium binding site 5 out of 6 in 8qkj

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Calcium binding site 5 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 133)


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

b:21.7
occ:1.00
 OD2 B:ASP345 2.3 25.0 1.0
OD1 B:ASP352 2.3 20.3 1.0
OE1 B:GLU336 2.3 17.9 1.0
O B:HOH1012 2.3 20.9 1.0
O B:VAL343 2.3 23.1 1.0
O B:ARG340 2.4 20.8 1.0
C B:ARG340 3.4 21.0 1.0
CD B:GLU336 3.5 21.4 1.0
CG B:ASP345 3.5 27.1 1.0
C B:VAL343 3.5 24.3 1.0
CG B:ASP352 3.6 23.8 1.0
N B:ARG340 3.8 22.4 1.0
N B:VAL343 3.9 23.7 1.0
OE2 B:GLU336 4.0 21.9 1.0
CA B:ASP352 4.1 19.7 1.0
N B:ASP352 4.1 20.7 1.0
CA B:VAL343 4.1 23.8 1.0
OD1 B:ASP345 4.2 27.7 1.0
CA B:ARG340 4.3 22.3 1.0
C B:GLY339 4.3 22.6 1.0
N B:ASP345 4.3 25.9 1.0
N B:LYS341 4.4 20.9 1.0
CB B:ASP352 4.4 20.4 1.0
O B:GLU336 4.4 19.6 1.0
CB B:VAL343 4.4 24.6 1.0
OD2 B:ASP352 4.5 25.2 1.0
CA B:LYS341 4.5 22.1 1.0
CB B:ASP345 4.5 25.9 1.0
N B:ASP344 4.6 25.1 1.0
CA B:GLY339 4.6 23.1 1.0
CA B:GLU336 4.6 19.5 1.0
CG B:GLU336 4.7 19.1 1.0
N B:GLY342 4.7 22.3 1.0
C B:LYS341 4.7 22.8 1.0
CB B:GLU336 4.8 18.8 1.0
CA B:ASP344 4.9 25.6 1.0
O B:GLY339 4.9 22.1 1.0
C B:GLU336 5.0 19.7 1.0

Calcium binding site 6 out of 6 in 8qkj

Go back to Calcium Binding Sites List in 8qkj
Calcium binding site 6 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Mam- 133)


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

b:22.1
occ:1.00
 O B:VAL350 2.2 24.7 1.0
OD1 B:ASP353 2.3 22.5 1.0
OD1 B:ASP346 2.3 27.7 1.0
OE2 B:GLU336 2.3 21.9 1.0
OD1 B:ASN348 2.4 25.0 1.0
OD1 B:ASP344 2.4 27.0 1.0
CG B:ASN348 3.3 26.9 1.0
CD B:GLU336 3.4 21.4 1.0
CG B:ASP344 3.4 28.9 1.0
CG B:ASP353 3.4 22.4 1.0
C B:VAL350 3.4 24.8 1.0
CG B:ASP346 3.5 29.2 1.0
CG B:GLU336 3.7 19.1 1.0
ND2 B:ASN348 3.7 26.5 1.0
OD2 B:ASP346 3.9 31.0 1.0
OD2 B:ASP353 4.0 22.8 1.0
CA B:ASP344 4.1 25.6 1.0
N B:VAL350 4.1 27.6 1.0
CA B:VAL350 4.2 26.1 1.0
OD2 B:ASP344 4.2 30.5 1.0
CB B:ASP344 4.2 26.4 1.0
N B:ASN348 4.3 29.6 1.0
CB B:VAL350 4.4 26.5 1.0
C B:ASP344 4.4 26.6 1.0
N B:ASP346 4.4 28.1 1.0
N B:VAL351 4.5 23.5 1.0
OE1 B:GLU336 4.5 17.9 1.0
ND2 B:ASN333 4.5 21.7 1.0
CB B:ASN348 4.5 27.8 1.0
N B:ASP353 4.5 18.7 1.0
N B:ASP345 4.5 25.9 1.0
CB B:ASP353 4.6 19.2 1.0
N B:ASP352 4.7 20.7 1.0
CA B:VAL351 4.7 23.1 1.0
CB B:ASP346 4.7 27.2 1.0
CA B:ASN348 4.8 28.7 1.0
N B:SER347 4.8 28.9 1.0
C B:VAL351 4.9 21.9 1.0
CA B:ASP346 4.9 28.2 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 11:17:44 2024

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