Atomistry » Chlorine » PDB 5r9a-5rad » 5r9u
Atomistry »
  Chlorine »
    PDB 5r9a-5rad »
      5r9u »

Chlorine in PDB 5r9u: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha:
2.7.11.24;

Protein crystallography data

The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha, PDB code: 5r9u was solved by G.F.De Nicola, C.E.Nichols, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.33 / 1.67
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.039, 86.958, 126.770, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 21.3

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha (pdb code 5r9u). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha, PDB code: 5r9u:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5r9u

Go back to Chlorine Binding Sites List in 5r9u
Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:43.7
occ:1.00
 O A:HOH726 2.8 29.9 1.0
O A:HOH634 2.9 31.4 1.0
O A:HOH689 3.0 38.0 1.0
N A:ARG23 3.0 22.8 1.0
N A:GLU22 3.5 24.6 1.0
CB A:ARG23 3.6 30.7 1.0
CB A:PRO6 3.8 33.1 1.0
CB A:PRO21 3.8 20.8 1.0
CA A:ARG23 3.9 25.0 1.0
C A:GLU22 3.9 21.6 1.0
CB A:GLU22 3.9 23.5 1.0
CA A:GLU22 3.9 24.2 1.0
C A:PRO21 4.0 22.2 1.0
CG A:ARG23 4.1 29.6 1.0
CA A:PRO21 4.3 21.4 1.0
O A:THR7 4.3 27.8 1.0
CD A:ARG23 4.7 27.0 1.0
CG A:GLU22 4.7 26.3 1.0
O A:PRO21 4.8 21.9 1.0
CA A:PRO6 4.8 32.6 1.0
O A:HOH676 4.9 32.5 1.0
CG A:PRO6 4.9 35.0 1.0
N A:THR7 4.9 26.3 1.0
OE1 A:GLU22 5.0 26.2 1.0

Chlorine binding site 2 out of 5 in 5r9u

Go back to Chlorine Binding Sites List in 5r9u
Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:47.7
occ:1.00
 N A:ASP101 3.2 32.7 1.0
N A:ASN100 3.3 34.3 1.0
OG1 A:THR91 3.4 28.1 1.0
CB A:ALA93 3.8 31.5 1.0
O A:GLU98 3.8 38.7 1.0
CB A:ASP101 3.9 32.8 1.0
N A:ALA93 3.9 29.6 1.0
CA A:ASN100 4.0 35.9 1.0
C A:ASN100 4.0 36.7 1.0
CA A:ASP101 4.0 29.4 1.0
O A:ASP101 4.1 29.6 1.0
CB A:ASN100 4.1 43.1 1.0
CG A:PRO92 4.1 29.9 1.0
CD A:PRO92 4.1 26.7 1.0
C A:PHE99 4.2 36.1 1.0
CA A:PHE99 4.3 33.2 1.0
CA A:ALA93 4.3 33.4 1.0
OD2 A:ASP101 4.4 42.8 1.0
CG A:ASP101 4.5 40.3 1.0
C A:ASP101 4.5 26.8 1.0
N A:PRO92 4.6 26.8 1.0
C A:GLU98 4.8 40.9 1.0
C A:PRO92 4.8 30.3 1.0
CB A:THR91 4.8 25.8 1.0
CD1 A:PHE99 4.9 26.2 1.0
ND2 A:ASN100 5.0 52.0 1.0
CB A:PRO92 5.0 28.4 1.0
N A:PHE99 5.0 35.1 1.0

Chlorine binding site 3 out of 5 in 5r9u

Go back to Chlorine Binding Sites List in 5r9u
Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:79.4
occ:1.00
 O A:HOH512 2.9 46.8 1.0
O A:HOH607 2.9 37.1 1.0
N A:GLY85 3.3 25.9 1.0
CE A:LYS165 3.4 36.4 0.4
ND1 A:HIS107 3.5 39.3 0.4
NZ A:LYS165 3.5 37.3 0.4
CD A:LYS165 3.7 33.2 0.4
CA A:GLY85 4.0 27.0 1.0
CB A:HIS107 4.1 33.3 0.4
O A:VAL83 4.1 22.6 1.0
C A:ILE84 4.2 24.9 1.0
CA A:ILE84 4.2 22.0 1.0
O A:GLY85 4.2 24.0 1.0
CG A:HIS107 4.2 35.0 0.4
CD1 A:ILE84 4.5 36.0 1.0
CE1 A:HIS107 4.5 37.0 0.4
C A:GLY85 4.5 25.5 1.0
O A:HOH562 4.8 24.9 1.0
C A:VAL83 5.0 20.5 1.0
N A:HIS107 5.0 29.2 0.4

Chlorine binding site 4 out of 5 in 5r9u

Go back to Chlorine Binding Sites List in 5r9u
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:41.5
occ:1.00
 N A:ASP324 3.0 24.8 1.0
CB A:ASP324 3.6 26.7 1.0
NH2 A:ARG73 3.6 24.9 1.0
CA A:TYR323 3.7 25.2 1.0
O A:PRO322 3.8 27.5 1.0
C A:TYR323 3.8 25.3 1.0
CA A:ASP324 3.9 25.5 1.0
CD1 A:TYR323 4.3 28.0 1.0
O A:ASP324 4.4 27.3 1.0
C A:PRO322 4.4 23.7 1.0
N A:TYR323 4.4 23.8 1.0
O A:HOH714 4.5 28.6 1.0
O A:HOH699 4.5 43.6 1.0
O A:HOH523 4.5 31.6 1.0
C A:ASP324 4.6 23.0 1.0
CD2 A:HIS77 4.7 25.9 1.0
NE2 A:HIS77 4.8 32.5 1.0
CZ A:ARG73 4.8 25.2 1.0
CB A:TYR323 4.9 25.8 1.0
CG A:TYR323 5.0 25.9 1.0

Chlorine binding site 5 out of 5 in 5r9u

Go back to Chlorine Binding Sites List in 5r9u
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13475A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:34.8
occ:1.00
 O A:HOH606 2.9 31.5 1.0
ND2 A:ASN114 3.2 50.9 0.4
N A:SER154 3.3 22.8 1.0
OG A:SER154 3.4 24.8 1.0
CB A:SER154 3.5 22.8 1.0
CD A:PRO153 3.6 21.4 1.0
N A:PRO153 3.8 19.8 1.0
CG A:LYS152 3.9 22.3 1.0
CB A:LYS152 3.9 20.8 1.0
CA A:SER154 4.0 25.3 1.0
CD A:LYS152 4.0 25.4 1.0
CG A:ASN114 4.1 47.4 0.4
OD1 A:ASN114 4.1 50.6 0.4
C A:PRO153 4.2 20.7 1.0
O A:HOH661 4.2 49.3 1.0
CB A:ALA184 4.2 23.9 1.0
CB A:PRO153 4.2 23.3 1.0
CA A:PRO153 4.3 20.1 1.0
C A:LYS152 4.3 19.9 1.0
CE1 A:TYR188 4.4 17.3 1.0
CG A:PRO153 4.4 21.0 1.0
CA A:LYS152 4.7 19.6 1.0
OH A:TYR188 4.8 21.8 1.0
CE A:LYS152 4.9 29.2 1.0
CZ A:TYR188 4.9 19.9 1.0

Reference:

C.Nichols, J.Ng, A.Keshu, G.Kelly, M.R.Conte, M.S.Marber, F.Fraternali, G.F.De Nicola. Mining the Pdb For Tractable Cases Where X-Ray Crystallography Combined with Fragment Screens Can Be Used to Systematically Design Protein-Protein Inhibitors: Two Test Cases Illustrated By IL1 Beta-IL1R and P38 Alpha-TAB1 Complexes. J.Med.Chem. V. 63 7559 2020.
ISSN: ISSN 0022-2623
PubMed: 32543856
DOI: 10.1021/ACS.JMEDCHEM.0C00403
Page generated: Fri Jul 26 16:10:37 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy