Chlorine in PDB 5r8z: Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N01381C in Complex with Map Kinase P38-Alpha
Enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N01381C in Complex with Map Kinase P38-Alpha
All present enzymatic activity of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N01381C 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 N01381C in Complex with Map Kinase P38-Alpha, PDB code: 5r8z
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)
|
51.12 /
1.65
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.860,
86.880,
126.460,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18 /
19.4
|
Other elements in 5r8z:
The structure of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N01381C in Complex with Map Kinase P38-Alpha also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N01381C in Complex with Map Kinase P38-Alpha
(pdb code 5r8z). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N01381C in Complex with Map Kinase P38-Alpha, PDB code: 5r8z:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 5r8z
Go back to
Chlorine Binding Sites List in 5r8z
Chlorine binding site 1 out
of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N01381C 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 N01381C in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl402
b:43.5
occ:1.00
|
O
|
A:HOH833
|
2.7
|
34.9
|
1.0
|
O
|
A:HOH591
|
3.0
|
30.6
|
1.0
|
N
|
A:ARG23
|
3.0
|
23.0
|
1.0
|
O
|
A:HOH786
|
3.2
|
37.7
|
1.0
|
N
|
A:GLU22
|
3.4
|
25.4
|
1.0
|
CB
|
A:ARG23
|
3.6
|
28.5
|
1.0
|
CB
|
A:PRO6
|
3.7
|
33.2
|
1.0
|
CB
|
A:PRO21
|
3.8
|
21.1
|
1.0
|
CA
|
A:ARG23
|
3.9
|
25.1
|
1.0
|
C
|
A:GLU22
|
3.9
|
21.2
|
1.0
|
CB
|
A:GLU22
|
3.9
|
23.3
|
1.0
|
CA
|
A:GLU22
|
3.9
|
23.0
|
1.0
|
CG
|
A:ARG23
|
4.0
|
24.4
|
1.0
|
C
|
A:PRO21
|
4.0
|
24.0
|
1.0
|
CA
|
A:PRO21
|
4.3
|
22.5
|
1.0
|
CD
|
A:ARG23
|
4.4
|
24.6
|
1.0
|
O
|
A:THR7
|
4.4
|
27.7
|
1.0
|
O
|
A:HOH752
|
4.6
|
34.1
|
1.0
|
CA
|
A:PRO6
|
4.8
|
31.1
|
1.0
|
O
|
A:PRO21
|
4.8
|
20.5
|
1.0
|
CG
|
A:PRO6
|
4.8
|
35.0
|
1.0
|
CG
|
A:GLU22
|
4.8
|
28.1
|
1.0
|
N
|
A:THR7
|
4.9
|
26.5
|
1.0
|
OE1
|
A:GLU22
|
4.9
|
27.1
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 5r8z
Go back to
Chlorine Binding Sites List in 5r8z
Chlorine binding site 2 out
of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N01381C 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 N01381C in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl403
b:41.4
occ:1.00
|
N
|
A:ASN100
|
3.2
|
31.4
|
1.0
|
N
|
A:ASP101
|
3.2
|
28.2
|
1.0
|
OG1
|
A:THR91
|
3.4
|
26.1
|
1.0
|
O
|
A:GLU98
|
3.7
|
35.0
|
1.0
|
CB
|
A:ALA93
|
3.7
|
24.9
|
1.0
|
N
|
A:ALA93
|
3.9
|
27.0
|
1.0
|
CA
|
A:ASN100
|
3.9
|
27.0
|
1.0
|
CB
|
A:ASP101
|
4.0
|
27.5
|
1.0
|
C
|
A:ASN100
|
4.0
|
29.4
|
1.0
|
CG
|
A:PRO92
|
4.0
|
32.6
|
1.0
|
CA
|
A:ASP101
|
4.1
|
26.0
|
1.0
|
O
|
A:ASP101
|
4.1
|
27.6
|
1.0
|
CB
|
A:ASN100
|
4.1
|
39.4
|
1.0
|
CD
|
A:PRO92
|
4.1
|
24.9
|
1.0
|
C
|
A:PHE99
|
4.2
|
33.0
|
1.0
|
CA
|
A:ALA93
|
4.2
|
28.2
|
1.0
|
CA
|
A:PHE99
|
4.2
|
28.7
|
1.0
|
C
|
A:ASP101
|
4.6
|
22.9
|
1.0
|
N
|
A:PRO92
|
4.6
|
24.9
|
1.0
|
CG
|
A:ASP101
|
4.6
|
38.5
|
1.0
|
OD2
|
A:ASP101
|
4.6
|
36.9
|
1.0
|
C
|
A:GLU98
|
4.7
|
36.6
|
1.0
|
CD1
|
A:PHE99
|
4.7
|
23.6
|
1.0
|
C
|
A:PRO92
|
4.7
|
29.3
|
1.0
|
ND2
|
A:ASN100
|
4.8
|
47.7
|
1.0
|
CB
|
A:THR91
|
4.8
|
24.5
|
1.0
|
CG
|
A:ASN100
|
4.9
|
53.3
|
1.0
|
N
|
A:PHE99
|
4.9
|
34.2
|
1.0
|
CB
|
A:PRO92
|
5.0
|
26.4
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 5r8z
Go back to
Chlorine Binding Sites List in 5r8z
Chlorine binding site 3 out
of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N01381C 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 N01381C in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl404
b:54.8
occ:1.00
|
O
|
A:HOH512
|
2.8
|
39.6
|
1.0
|
O
|
A:HOH505
|
2.8
|
38.9
|
1.0
|
CE
|
A:LYS165
|
3.4
|
42.1
|
1.0
|
N
|
A:GLY85
|
3.4
|
21.9
|
1.0
|
CD
|
A:LYS165
|
3.5
|
30.7
|
1.0
|
NZ
|
A:LYS165
|
3.5
|
43.5
|
1.0
|
CD2
|
A:HIS107
|
3.6
|
32.2
|
1.0
|
O
|
A:VAL83
|
4.0
|
21.1
|
1.0
|
CA
|
A:ILE84
|
4.1
|
19.7
|
1.0
|
C
|
A:ILE84
|
4.2
|
23.4
|
1.0
|
CA
|
A:GLY85
|
4.2
|
24.8
|
1.0
|
CE
|
A:MET109
|
4.3
|
47.9
|
1.0
|
O
|
A:GLY85
|
4.4
|
21.8
|
1.0
|
CG
|
A:HIS107
|
4.4
|
31.1
|
1.0
|
CB
|
A:HIS107
|
4.5
|
32.1
|
1.0
|
C
|
A:GLY85
|
4.7
|
23.0
|
1.0
|
NE2
|
A:HIS107
|
4.7
|
38.2
|
1.0
|
O
|
A:HOH792
|
4.7
|
39.3
|
1.0
|
C
|
A:VAL83
|
4.8
|
18.9
|
1.0
|
CG1
|
A:ILE84
|
4.9
|
24.2
|
1.0
|
N
|
A:ILE84
|
4.9
|
18.2
|
1.0
|
CG
|
A:LYS165
|
4.9
|
27.1
|
1.0
|
O
|
A:HOH628
|
4.9
|
21.2
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 5r8z
Go back to
Chlorine Binding Sites List in 5r8z
Chlorine binding site 4 out
of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N01381C 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 N01381C in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl405
b:28.6
occ:0.57
|
O
|
A:HOH633
|
2.8
|
34.0
|
1.0
|
N
|
A:ASP324
|
3.0
|
24.1
|
1.0
|
NH2
|
A:ARG73
|
3.5
|
23.6
|
1.0
|
CB
|
A:ASP324
|
3.6
|
22.8
|
1.0
|
O
|
A:PRO322
|
3.7
|
23.3
|
1.0
|
CA
|
A:TYR323
|
3.8
|
25.5
|
1.0
|
CA
|
A:ASP324
|
3.8
|
23.1
|
1.0
|
C
|
A:TYR323
|
3.9
|
26.2
|
1.0
|
O
|
A:ASP324
|
4.3
|
23.8
|
1.0
|
CD1
|
A:TYR323
|
4.4
|
23.1
|
1.0
|
C
|
A:PRO322
|
4.5
|
23.9
|
1.0
|
N
|
A:TYR323
|
4.5
|
22.8
|
1.0
|
C
|
A:ASP324
|
4.6
|
22.4
|
1.0
|
O
|
A:HOH821
|
4.6
|
26.1
|
1.0
|
O
|
A:HOH812
|
4.6
|
42.2
|
1.0
|
O
|
A:HOH624
|
4.6
|
30.8
|
1.0
|
CZ
|
A:ARG73
|
4.7
|
22.8
|
1.0
|
ND1
|
A:HIS77
|
4.7
|
30.6
|
1.0
|
CE1
|
A:HIS77
|
4.8
|
29.0
|
1.0
|
CB
|
A:TYR323
|
4.9
|
23.5
|
1.0
|
CG
|
A:TYR323
|
5.0
|
21.9
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 5r8z
Go back to
Chlorine Binding Sites List in 5r8z
Chlorine binding site 5 out
of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N01381C 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 N01381C in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl406
b:31.1
occ:1.00
|
O
|
A:HOH675
|
2.8
|
36.0
|
1.0
|
O
|
A:HOH595
|
3.0
|
30.0
|
1.0
|
N
|
A:SER154
|
3.2
|
20.1
|
1.0
|
OG
|
A:SER154
|
3.3
|
23.3
|
1.0
|
CB
|
A:SER154
|
3.5
|
22.1
|
1.0
|
CD
|
A:PRO153
|
3.7
|
16.8
|
1.0
|
N
|
A:PRO153
|
3.7
|
16.4
|
1.0
|
CG
|
A:LYS152
|
3.8
|
20.7
|
1.0
|
CB
|
A:LYS152
|
3.9
|
19.9
|
1.0
|
CA
|
A:SER154
|
4.0
|
21.7
|
1.0
|
CD
|
A:LYS152
|
4.1
|
19.0
|
1.0
|
CB
|
A:PRO153
|
4.1
|
21.6
|
1.0
|
C
|
A:PRO153
|
4.1
|
19.5
|
1.0
|
CG
|
A:ASN114
|
4.2
|
49.3
|
1.0
|
CA
|
A:PRO153
|
4.2
|
17.5
|
1.0
|
CB
|
A:ALA184
|
4.2
|
25.8
|
1.0
|
C
|
A:LYS152
|
4.3
|
17.8
|
1.0
|
OD1
|
A:ASN114
|
4.3
|
53.7
|
1.0
|
CG
|
A:PRO153
|
4.4
|
19.7
|
1.0
|
ND2
|
A:ASN114
|
4.4
|
54.9
|
1.0
|
CE1
|
A:TYR188
|
4.4
|
18.6
|
1.0
|
CB
|
A:ASN114
|
4.5
|
38.2
|
1.0
|
CA
|
A:LYS152
|
4.7
|
17.8
|
1.0
|
OH
|
A:TYR188
|
4.7
|
22.6
|
1.0
|
O
|
A:HOH502
|
4.8
|
40.7
|
1.0
|
CE
|
A:LYS152
|
4.9
|
24.3
|
1.0
|
CZ
|
A:TYR188
|
4.9
|
20.9
|
1.0
|
O
|
A:LYS152
|
5.0
|
18.9
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 5r8z
Go back to
Chlorine Binding Sites List in 5r8z
Chlorine binding site 6 out
of 6 in the Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N01381C 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 6 of Pandda Analysis Group Deposition FORM1 Map Kinase P38-Alpha -- Fragment N01381C in Complex with Map Kinase P38-Alpha within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl407
b:40.5
occ:1.00
|
O
|
A:HOH661
|
2.9
|
42.3
|
1.0
|
NH2
|
A:ARG189
|
3.2
|
36.8
|
1.0
|
N
|
A:HIS174
|
3.4
|
34.4
|
1.0
|
O
|
A:HOH715
|
3.5
|
49.9
|
1.0
|
CD2
|
A:HIS174
|
3.6
|
28.8
|
1.0
|
NE
|
A:ARG149
|
3.7
|
41.8
|
1.0
|
NH1
|
A:ARG189
|
3.8
|
40.0
|
1.0
|
CB
|
A:HIS174
|
4.0
|
32.1
|
1.0
|
CZ
|
A:ARG189
|
4.0
|
36.6
|
1.0
|
CG
|
A:HIS174
|
4.1
|
29.9
|
1.0
|
CA
|
A:ARG173
|
4.2
|
37.3
|
1.0
|
O
|
A:HOH711
|
4.2
|
27.2
|
1.0
|
O
|
A:HOH702
|
4.2
|
23.6
|
1.0
|
C
|
A:ARG173
|
4.3
|
35.4
|
1.0
|
CA
|
A:HIS174
|
4.3
|
35.2
|
1.0
|
CB
|
A:ARG173
|
4.6
|
43.6
|
1.0
|
CG
|
A:ARG173
|
4.6
|
46.0
|
1.0
|
CB
|
A:ARG149
|
4.7
|
25.1
|
1.0
|
NE2
|
A:HIS174
|
4.8
|
25.6
|
1.0
|
CD
|
A:ARG149
|
4.9
|
37.7
|
1.0
|
O
|
A:HIS174
|
5.0
|
37.9
|
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 15:56:04 2024
|