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Calcium in PDB 9fm5: PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Al- 97)

Enzymatic activity of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Al- 97)

All present enzymatic activity of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Al- 97):
3.4.21.62;

Protein crystallography data

The structure of PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Al- 97), PDB code: 9fm5 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) 22.87 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.201, 106.067, 72.159, 90, 90.51, 90
R / Rfree (%) 19.6 / 22.4

Calcium Binding Sites:

The binding sites of Calcium atom in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Al- 97) (pdb code 9fm5). 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 (Al- 97), PDB code: 9fm5:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 9fm5

Go back to Calcium Binding Sites List in 9fm5
Calcium binding site 1 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Al- 97)


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 (Al- 97) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:14.1
occ:1.00
 O A:VAL383 2.3 16.7 1.0
OD2 A:ASP281 2.3 15.5 1.0
OD1 A:ASP325 2.4 14.6 1.0
O A:ILE388 2.4 15.1 1.0
O A:ILE390 2.4 14.5 1.0
OD1 A:ASN386 2.5 15.6 1.0
OD2 A:ASP325 2.6 15.9 1.0
CG A:ASP325 2.8 14.2 1.0
CG A:ASP281 3.4 16.7 1.0
CG A:ASN386 3.5 17.2 1.0
C A:VAL383 3.5 16.2 1.0
C A:ILE390 3.5 14.2 1.0
C A:ILE388 3.6 15.5 1.0
N A:ILE390 3.7 14.0 1.0
ND2 A:ASN386 3.8 18.1 1.0
C A:GLY389 4.0 14.6 1.0
CB A:ASP281 4.1 15.2 1.0
CA A:ILE390 4.3 13.6 1.0
CA A:GLY389 4.3 13.8 1.0
CA A:GLY384 4.3 16.3 1.0
N A:GLY384 4.3 15.9 1.0
CB A:ASP325 4.4 15.0 1.0
N A:GLY389 4.4 14.8 1.0
CA A:VAL383 4.5 14.7 1.0
CG1 A:ILE388 4.5 17.2 1.0
OD1 A:ASP281 4.5 15.9 1.0
N A:VAL383 4.5 14.1 1.0
N A:ILE388 4.6 16.3 1.0
CA A:ILE388 4.6 15.8 1.0
N A:VAL391 4.6 13.6 1.0
O A:GLY389 4.7 15.3 1.0
N A:ASN386 4.8 17.9 1.0
CB A:VAL383 4.8 14.9 1.0
CB A:ASN386 4.8 16.8 1.0
C A:GLY384 4.9 17.8 1.0
CA A:VAL391 4.9 13.8 1.0
C A:ALA382 4.9 14.2 1.0
N A:ASN385 5.0 17.0 1.0

Calcium binding site 2 out of 6 in 9fm5

Go back to Calcium Binding Sites List in 9fm5
Calcium binding site 2 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Al- 97)


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 (Al- 97) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca902

b:15.6
occ:1.00
 OD1 A:ASP346 2.3 20.0 1.0
O A:VAL350 2.3 17.6 1.0
OE2 A:GLU336 2.3 16.9 1.0
OD1 A:ASN348 2.4 16.6 1.0
OD1 A:ASP353 2.4 14.4 1.0
OD1 A:ASP344 2.4 16.5 1.0
CG A:ASN348 3.3 18.3 1.0
CD A:GLU336 3.4 17.3 1.0
CG A:ASP346 3.4 20.4 1.0
CG A:ASP344 3.5 20.3 1.0
CG A:ASP353 3.5 16.5 1.0
C A:VAL350 3.5 17.1 1.0
CG A:GLU336 3.7 13.6 1.0
ND2 A:ASN348 3.7 18.3 1.0
OD2 A:ASP346 3.9 22.9 1.0
OD2 A:ASP353 3.9 17.4 1.0
CA A:ASP344 4.1 16.4 1.0
N A:VAL350 4.2 17.4 1.0
CB A:ASP344 4.2 18.2 1.0
OD2 A:ASP344 4.3 21.1 1.0
CA A:VAL350 4.3 17.6 1.0
N A:ASN348 4.3 19.0 1.0
C A:ASP344 4.4 16.2 1.0
N A:ASP346 4.4 15.8 1.0
ND2 A:ASN333 4.4 18.7 1.0
CB A:ASN348 4.5 17.4 1.0
OE1 A:GLU336 4.5 14.8 1.0
N A:ASP345 4.5 15.0 1.0
N A:ASP352 4.6 15.4 1.0
N A:VAL351 4.6 16.2 1.0
CB A:VAL350 4.6 18.6 1.0
N A:ASP353 4.6 14.4 1.0
CB A:ASP346 4.7 17.6 1.0
CA A:VAL351 4.7 15.3 1.0
CB A:ASP353 4.7 14.4 1.0
CA A:ASN348 4.8 18.5 1.0
N A:SER347 4.8 19.1 1.0
C A:VAL351 4.9 16.0 1.0
CA A:ASP346 4.9 17.8 1.0
N A:GLY349 5.0 20.1 1.0
O A:ASP344 5.0 16.1 1.0

Calcium binding site 3 out of 6 in 9fm5

Go back to Calcium Binding Sites List in 9fm5
Calcium binding site 3 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Al- 97)


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 (Al- 97) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:15.2
occ:1.00
 OD1 A:ASP352 2.3 16.0 1.0
OD1 A:ASP345 2.3 19.3 1.0
O A:VAL343 2.3 17.5 1.0
O A:HOH1047 2.3 18.3 1.0
OE1 A:GLU336 2.3 14.8 1.0
O A:ARG340 2.4 15.9 1.0
C A:ARG340 3.4 17.3 1.0
CD A:GLU336 3.4 17.3 1.0
C A:VAL343 3.5 16.9 1.0
CG A:ASP352 3.5 17.9 1.0
CG A:ASP345 3.5 20.1 1.0
N A:ARG340 3.9 18.4 1.0
CA A:ASP352 4.0 14.8 1.0
N A:VAL343 4.0 17.5 1.0
OE2 A:GLU336 4.0 16.9 1.0
N A:ASP352 4.0 15.4 1.0
CA A:VAL343 4.1 16.8 1.0
OD2 A:ASP345 4.2 23.1 1.0
CA A:ARG340 4.3 17.6 1.0
CB A:ASP352 4.3 16.2 1.0
N A:ASP345 4.3 15.0 1.0
N A:LYS341 4.3 16.4 1.0
CB A:VAL343 4.3 17.2 1.0
OD2 A:ASP352 4.4 18.9 1.0
CA A:LYS341 4.4 16.9 1.0
O A:GLU336 4.4 15.8 1.0
C A:GLY339 4.5 19.1 1.0
N A:ASP344 4.6 16.6 1.0
CB A:ASP345 4.6 16.2 1.0
CA A:GLU336 4.6 14.5 1.0
CG A:GLU336 4.6 13.6 1.0
N A:GLY342 4.6 17.8 1.0
C A:LYS341 4.7 17.8 1.0
CB A:GLU336 4.7 13.4 1.0
CA A:GLY339 4.8 19.6 1.0
CA A:ASP344 4.8 16.4 1.0

Calcium binding site 4 out of 6 in 9fm5

Go back to Calcium Binding Sites List in 9fm5
Calcium binding site 4 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Al- 97)


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 (Al- 97) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca901

b:15.7
occ:1.00
 OD2 B:ASP281 2.3 18.5 1.0
O B:VAL383 2.3 16.9 1.0
O B:ILE390 2.4 14.4 1.0
O B:ILE388 2.4 16.1 1.0
OD1 B:ASP325 2.4 17.8 1.0
OD1 B:ASN386 2.4 17.9 1.0
OD2 B:ASP325 2.7 19.5 1.0
CG B:ASP325 2.9 17.8 1.0
CG B:ASP281 3.4 17.4 1.0
CG B:ASN386 3.4 19.5 1.0
C B:VAL383 3.5 17.5 1.0
C B:ILE390 3.6 14.0 1.0
C B:ILE388 3.6 16.3 1.0
N B:ILE390 3.8 14.3 1.0
ND2 B:ASN386 3.8 21.0 1.0
CB B:ASP281 4.0 16.6 1.0
C B:GLY389 4.1 14.7 1.0
CA B:ILE390 4.3 13.6 1.0
CA B:GLY384 4.4 17.9 1.0
CA B:GLY389 4.4 14.7 1.0
N B:GLY384 4.4 17.3 1.0
CB B:ASP325 4.4 15.2 1.0
N B:GLY389 4.4 14.5 1.0
CG1 B:ILE388 4.4 19.5 1.0
OD1 B:ASP281 4.5 18.0 1.0
CA B:VAL383 4.5 16.1 1.0
N B:ILE388 4.5 19.0 1.0
N B:VAL383 4.5 16.1 1.0
CA B:ILE388 4.6 18.1 1.0
O B:GLY389 4.6 15.9 1.0
N B:VAL391 4.6 13.9 1.0
N B:ASN386 4.7 18.7 1.0
CB B:VAL383 4.7 17.2 1.0
CB B:ASN386 4.8 19.0 1.0
C B:GLY384 4.9 19.1 1.0
CA B:VAL391 4.9 14.1 1.0
C B:ALA382 4.9 16.2 1.0
N B:ASN385 5.0 17.9 1.0

Calcium binding site 5 out of 6 in 9fm5

Go back to Calcium Binding Sites List in 9fm5
Calcium binding site 5 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Al- 97)


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 (Al- 97) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca902

b:17.1
occ:1.00
 OD1 B:ASP346 2.3 22.1 1.0
OE2 B:GLU336 2.3 20.4 1.0
OD1 B:ASP353 2.3 14.7 1.0
OD1 B:ASP344 2.4 20.1 1.0
O B:VAL350 2.4 16.6 1.0
OD1 B:ASN348 2.4 20.0 1.0
CG B:ASN348 3.3 20.1 1.0
CD B:GLU336 3.3 19.1 1.0
CG B:ASP346 3.4 23.6 1.0
CG B:ASP353 3.5 17.7 1.0
CG B:ASP344 3.5 21.9 1.0
C B:VAL350 3.6 16.9 1.0
ND2 B:ASN348 3.7 19.6 1.0
CG B:GLU336 3.7 16.6 1.0
OD2 B:ASP346 3.9 25.1 1.0
OD2 B:ASP353 4.0 20.1 1.0
CA B:ASP344 4.0 18.6 1.0
CB B:ASP344 4.2 19.4 1.0
N B:VAL350 4.2 20.0 1.0
CA B:VAL350 4.3 18.2 1.0
N B:ASP346 4.3 24.3 1.0
C B:ASP344 4.3 20.7 1.0
N B:ASN348 4.3 24.3 1.0
OD2 B:ASP344 4.4 22.9 1.0
OE1 B:GLU336 4.4 15.9 1.0
N B:ASP345 4.5 21.5 1.0
CB B:VAL350 4.5 18.9 1.0
ND2 B:ASN333 4.5 19.2 1.0
CB B:ASN348 4.5 20.7 1.0
N B:ASP353 4.6 14.7 1.0
N B:VAL351 4.6 16.1 1.0
N B:ASP352 4.6 15.1 1.0
CB B:ASP353 4.7 15.3 1.0
CB B:ASP346 4.7 23.4 1.0
CA B:VAL351 4.7 15.4 1.0
CA B:ASN348 4.8 22.6 1.0
N B:SER347 4.8 25.8 1.0
CA B:ASP346 4.9 24.2 1.0
C B:VAL351 4.9 15.0 1.0
O B:ASP344 4.9 21.7 1.0
C B:ASP346 5.0 25.8 1.0

Calcium binding site 6 out of 6 in 9fm5

Go back to Calcium Binding Sites List in 9fm5
Calcium binding site 6 out of 6 in the PVSUB1 Catalytic Domain in Complex with Peptidomimetic Inhibitor (Al- 97)


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 (Al- 97) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca903

b:16.6
occ:1.00
 OD1 B:ASP345 2.2 23.8 1.0
O B:VAL343 2.3 18.7 1.0
OE1 B:GLU336 2.3 15.9 1.0
OD1 B:ASP352 2.4 17.4 1.0
O B:ARG340 2.4 19.7 1.0
CG B:ASP345 3.4 26.7 1.0
C B:VAL343 3.4 18.5 1.0
C B:ARG340 3.5 20.9 1.0
CD B:GLU336 3.5 19.1 1.0
CG B:ASP352 3.6 18.1 1.0
N B:ARG340 3.9 21.9 1.0
OE2 B:GLU336 4.0 20.4 1.0
N B:VAL343 4.0 17.6 1.0
CA B:ASP352 4.1 15.0 1.0
N B:ASP352 4.1 15.1 1.0
OD2 B:ASP345 4.1 28.4 1.0
CA B:VAL343 4.1 18.1 1.0
N B:ASP345 4.2 21.5 1.0
CA B:ARG340 4.3 22.4 1.0
CB B:VAL343 4.3 19.0 1.0
C B:GLY339 4.3 22.6 1.0
N B:LYS341 4.4 19.6 1.0
CB B:ASP352 4.4 15.6 1.0
O B:GLU336 4.5 18.9 1.0
OD2 B:ASP352 4.5 19.7 1.0
CA B:LYS341 4.5 19.4 1.0
CB B:ASP345 4.5 23.4 1.0
N B:ASP344 4.5 18.6 1.0
O B:HOH1205 4.5 35.0 1.0
CA B:GLY339 4.6 23.1 1.0
CA B:GLU336 4.6 17.2 1.0
N B:GLY342 4.6 18.1 1.0
CG B:GLU336 4.7 16.6 1.0
C B:LYS341 4.7 19.5 1.0
CB B:GLU336 4.8 16.3 1.0
CA B:ASP344 4.8 18.6 1.0
O B:GLY339 4.9 23.1 1.0
CB B:ARG340 4.9 24.1 1.0

Reference:

A.K.Puszko, F.A.Batista, A.Ejjoummany, A.Bouillon, M.Maurel, P.Adler, A.Legru, M.Martinez, L.Ortega Varga, M.Hadjadj, P.M.Alzari, A.Blondel, A.Haouz, J.C.Barale, J.F.Hernandez. Towards Improved Peptidic Alpha-Ketoamide Inhibitors of the Plasmodial Subtilisin-Like SUB1: Exploration of N-Terminal Extensions and Cyclic Constraints. Chemmedchem 00924 2025.
ISSN: ESSN 1860-7187
PubMed: 39832214
DOI: 10.1002/CMDC.202400924
Page generated: Sun Feb 9 06:19:35 2025

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