Atomistry » Calcium » PDB 9dyn-9fzc » 9fm5
Atomistry »
  Calcium »
    PDB 9dyn-9fzc »
      9fm5 »

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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy