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Chlorine in PDB 5r9y: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A in Complex with Map Kinase P38-Alpha

Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A in Complex with Map Kinase P38-Alpha

All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A 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 N13619A in Complex with Map Kinase P38-Alpha, PDB code: 5r9y 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) 71.64 / 1.57
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.720, 87.210, 125.650, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 21

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A in Complex with Map Kinase P38-Alpha (pdb code 5r9y). 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 N13619A in Complex with Map Kinase P38-Alpha, PDB code: 5r9y:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5r9y

Go back to Chlorine Binding Sites List in 5r9y
Chlorine binding site 1 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A 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 N13619A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:42.0
occ:1.00
 O A:HOH736 2.8 31.1 1.0
O A:HOH703 2.9 34.6 1.0
O A:HOH594 3.0 29.5 1.0
N A:ARG23 3.1 21.3 1.0
N A:GLU22 3.5 21.2 1.0
CB A:ARG23 3.7 27.4 1.0
CB A:PRO6 3.7 34.4 1.0
CB A:PRO21 3.8 20.6 1.0
C A:GLU22 3.9 20.7 1.0
CA A:ARG23 3.9 22.9 1.0
CA A:GLU22 3.9 22.4 1.0
CB A:GLU22 3.9 21.8 1.0
C A:PRO21 4.0 19.3 1.0
CG A:ARG23 4.1 26.4 1.0
CA A:PRO21 4.3 20.2 1.0
O A:THR7 4.3 25.2 1.0
CD A:ARG23 4.5 26.5 1.0
CA A:PRO6 4.7 29.9 1.0
CG A:GLU22 4.7 26.1 1.0
O A:PRO21 4.8 20.0 1.0
CG A:PRO6 4.8 37.1 1.0
N A:THR7 4.9 26.2 1.0
O A:HOH683 4.9 31.2 1.0
OE1 A:GLU22 4.9 25.3 1.0
O A:GLU22 5.0 22.3 1.0

Chlorine binding site 2 out of 5 in 5r9y

Go back to Chlorine Binding Sites List in 5r9y
Chlorine binding site 2 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A 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 N13619A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:37.4
occ:1.00
 N A:ASP101 3.2 27.9 1.0
N A:ASN100 3.2 29.0 1.0
OG1 A:THR91 3.4 24.9 1.0
CB A:ALA93 3.7 26.0 1.0
O A:GLU98 3.7 34.6 1.0
N A:ALA93 3.8 25.1 1.0
CB A:ASP101 3.9 27.2 1.0
CA A:ASN100 4.0 30.3 1.0
CD A:PRO92 4.1 24.6 1.0
CG A:PRO92 4.1 30.7 1.0
C A:ASN100 4.1 30.9 1.0
CA A:ASP101 4.1 28.3 1.0
CA A:ALA93 4.1 26.5 1.0
O A:ASP101 4.1 26.2 1.0
CB A:ASN100 4.2 38.4 1.0
C A:PHE99 4.2 34.3 1.0
CA A:PHE99 4.2 29.3 1.0
N A:PRO92 4.6 25.8 1.0
CG A:ASP101 4.6 34.9 1.0
C A:ASP101 4.6 23.0 1.0
C A:PRO92 4.7 27.2 1.0
C A:GLU98 4.7 35.5 1.0
OD2 A:ASP101 4.7 36.6 1.0
ND2 A:ASN100 4.8 51.2 1.0
CD1 A:PHE99 4.8 25.3 1.0
CB A:THR91 4.8 22.8 1.0
CB A:PRO92 4.9 28.0 1.0
N A:PHE99 4.9 30.0 1.0
CA A:PRO92 5.0 28.1 1.0

Chlorine binding site 3 out of 5 in 5r9y

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Chlorine binding site 3 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A 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 N13619A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:71.5
occ:1.00
 ND1 A:HIS107 2.7 27.6 0.4
N A:GLY85 3.0 25.1 1.0
O A:HOH501 3.2 38.5 1.0
CE1 A:HIS107 3.4 27.9 0.4
CD A:LYS165 3.6 31.3 1.0
OG1 A:THR106 3.6 16.0 0.4
CE A:LYS165 3.6 39.5 1.0
O A:GLY85 3.8 27.7 1.0
CA A:ILE84 3.8 21.3 0.4
C A:ILE84 3.8 22.6 0.4
CG A:HIS107 3.8 26.6 0.4
NZ A:LYS165 3.9 48.8 1.0
CA A:GLY85 3.9 29.5 1.0
O A:VAL83 4.1 22.4 1.0
CB A:HIS107 4.2 26.6 0.4
C A:GLY85 4.3 26.4 1.0
N A:HIS107 4.5 22.5 0.4
NE2 A:HIS107 4.6 28.4 0.4
CG1 A:ILE84 4.6 21.7 0.4
N A:ILE84 4.7 19.6 0.4
CD2 A:HIS107 4.8 27.8 0.4
CB A:ILE84 4.8 20.9 0.4
C A:VAL83 4.8 19.3 1.0
O A:ILE84 4.9 22.8 0.4
CG A:LYS165 5.0 30.4 1.0
CB A:THR106 5.0 18.3 0.4
SD A:MET109 5.0 28.1 0.4

Chlorine binding site 4 out of 5 in 5r9y

Go back to Chlorine Binding Sites List in 5r9y
Chlorine binding site 4 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A 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 N13619A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:41.8
occ:1.00
 O A:HOH698 2.9 37.5 1.0
N A:ASP324 3.0 23.6 1.0
NH2 A:ARG73 3.6 24.3 1.0
CB A:ASP324 3.7 22.9 1.0
O A:PRO322 3.7 24.3 1.0
CA A:TYR323 3.8 23.3 1.0
C A:TYR323 3.9 24.5 1.0
CA A:ASP324 3.9 22.8 1.0
CD1 A:TYR323 4.3 25.9 1.0
O A:ASP324 4.4 24.7 1.0
C A:PRO322 4.5 22.6 1.0
O A:HOH513 4.5 31.5 1.0
N A:TYR323 4.5 21.7 1.0
O A:HOH725 4.5 28.2 1.0
C A:ASP324 4.7 22.0 1.0
CD2 A:HIS77 4.7 26.1 1.0
CZ A:ARG73 4.8 21.6 1.0
NE2 A:HIS77 4.8 30.0 1.0
CB A:TYR323 4.9 22.4 1.0
CG A:TYR323 4.9 21.6 1.0
CE1 A:TYR323 4.9 26.1 1.0

Chlorine binding site 5 out of 5 in 5r9y

Go back to Chlorine Binding Sites List in 5r9y
Chlorine binding site 5 out of 5 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N13619A 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 N13619A in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:31.9
occ:1.00
 O A:HOH620 3.0 34.3 1.0
N A:SER154 3.3 20.6 1.0
OG A:SER154 3.3 21.4 1.0
O A:HOH657 3.4 45.5 1.0
CB A:SER154 3.6 20.6 1.0
CD A:PRO153 3.7 19.3 1.0
ND2 A:ASN114 3.8 41.1 0.5
N A:PRO153 3.8 18.6 1.0
CG A:LYS152 3.9 21.4 1.0
CB A:LYS152 3.9 21.1 1.0
CA A:SER154 4.0 21.7 1.0
CD A:LYS152 4.0 24.7 1.0
C A:PRO153 4.2 19.7 1.0
CB A:PRO153 4.2 21.1 1.0
CA A:PRO153 4.3 18.2 1.0
CB A:ALA184 4.3 22.4 1.0
C A:LYS152 4.4 18.6 1.0
CE1 A:TYR188 4.4 16.3 1.0
CG A:PRO153 4.4 19.9 1.0
CG A:ASN114 4.7 42.1 0.5
OD1 A:ASN114 4.7 43.0 0.5
CA A:LYS152 4.7 18.5 1.0
OH A:TYR188 4.9 19.0 1.0
CE A:LYS152 4.9 26.8 1.0
CZ A:TYR188 4.9 18.2 1.0
O A:HOH506 4.9 39.2 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 16:11:19 2024

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