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Chlorine in PDB 5lvo: Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket

Enzymatic activity of Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket

All present enzymatic activity of Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket:
2.7.11.1;

Protein crystallography data

The structure of Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket, PDB code: 5lvo was solved by J.O.Schulze, G.Saladino, K.Busschots, S.Neimanis, E.Suess, D.Odadzic, S.Zeuzem, V.Hindie, A.K.Herbrand, M.N.Lisa, P.M.Alzari, F.L.Gervasio, R.M.Biondi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.54 / 1.09
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 148.220, 44.420, 47.870, 90.00, 101.81, 90.00
R / Rfree (%) 13.5 / 15.7

Other elements in 5lvo:

The structure of Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket also contains other interesting chemical elements:

Fluorine (F) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket (pdb code 5lvo). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket, PDB code: 5lvo:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5lvo

Go back to Chlorine Binding Sites List in 5lvo
Chlorine binding site 1 out of 3 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:34.1
occ:1.00
CL1 A:78W402 0.0 34.1 1.0
C5 A:78W402 1.8 31.6 1.0
C6 A:78W402 2.7 30.4 1.0
C4 A:78W402 2.7 29.6 1.0
HG13 A:ILE119 2.8 36.0 1.0
HG2 A:LYS115 3.0 30.9 1.0
HD11 A:LEU155 3.1 32.5 1.0
HG22 A:VAL124 3.1 28.9 1.0
HA A:LYS115 3.1 28.9 1.0
HB A:ILE118 3.3 27.0 1.0
HB3 A:LYS115 3.4 31.4 1.0
HD11 A:ILE119 3.5 37.3 1.0
HG21 A:ILE118 3.5 31.9 1.0
HG22 A:ILE118 3.5 31.9 1.0
CG1 A:ILE119 3.7 30.0 1.0
CG A:LYS115 3.8 25.8 1.0
CB A:LYS115 3.9 26.1 1.0
HG12 A:ILE119 3.9 36.0 1.0
CA A:LYS115 3.9 24.1 1.0
CG2 A:ILE118 3.9 26.6 1.0
O A:LYS115 3.9 25.7 1.0
CD1 A:ILE119 4.0 31.1 1.0
CG2 A:VAL124 4.0 24.1 1.0
C1 A:78W402 4.0 33.8 1.0
C3 A:78W402 4.0 31.8 1.0
CD1 A:LEU155 4.0 27.1 1.0
CB A:ILE118 4.0 22.5 1.0
HG21 A:VAL124 4.1 28.9 1.0
HD12 A:ILE119 4.1 37.3 1.0
HD21 A:LEU155 4.2 26.2 1.0
H A:ILE119 4.2 28.6 1.0
HD12 A:LEU155 4.3 32.5 1.0
C A:LYS115 4.3 25.8 1.0
HG23 A:VAL124 4.4 28.9 1.0
HE2 A:LYS115 4.4 32.4 1.0
HD3 A:LYS115 4.5 31.7 1.0
HG3 A:LYS115 4.5 30.9 1.0
C2 A:78W402 4.5 33.8 1.0
HG A:LEU155 4.5 22.7 1.0
N A:ILE119 4.5 23.8 1.0
HD13 A:LEU155 4.6 32.5 1.0
HG13 A:ILE118 4.7 26.2 1.0
CD A:LYS115 4.7 26.4 1.0
HG13 A:VAL124 4.7 26.8 1.0
CG A:LEU155 4.7 18.9 1.0
HB2 A:LYS115 4.8 31.4 1.0
HG23 A:ILE118 4.8 31.9 1.0
CB A:ILE119 4.9 29.1 1.0
HD13 A:ILE119 4.9 37.3 1.0
HA A:VAL124 4.9 22.9 1.0
HA A:ILE119 4.9 30.9 1.0
CD2 A:LEU155 4.9 21.8 1.0
CG1 A:ILE118 5.0 21.8 1.0

Chlorine binding site 2 out of 3 in 5lvo

Go back to Chlorine Binding Sites List in 5lvo
Chlorine binding site 2 out of 3 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:36.5
occ:1.00
CL2 A:78W402 0.0 36.5 1.0
C17 A:78W402 1.7 26.7 1.0
HG22 A:THR128 2.7 21.5 0.5
C12 A:78W402 2.7 25.8 1.0
C16 A:78W402 2.7 24.7 1.0
HG12 A:VAL127 2.8 29.7 1.0
HA A:THR128 2.9 17.9 0.5
HA A:THR128 3.0 16.6 0.5
C11 A:78W402 3.0 32.1 1.0
N10 A:78W402 3.1 35.3 1.0
HD3 A:ARG131 3.2 23.2 0.6
HD3 A:ARG131 3.3 22.7 0.4
CG2 A:THR128 3.5 17.9 0.5
HB2 A:ARG131 3.6 15.8 0.4
HG23 A:THR128 3.7 21.5 0.5
CG1 A:VAL127 3.7 24.7 1.0
HB2 A:ARG131 3.7 15.8 0.6
CA A:THR128 3.7 14.9 0.5
HB3 A:ARG131 3.7 15.8 0.6
HD2 A:ARG131 3.8 23.2 0.6
HB3 A:ARG131 3.8 15.8 0.4
O A:VAL127 3.8 13.8 1.0
CA A:THR128 3.8 13.9 0.5
O20 A:78W402 3.9 36.5 1.0
HG11 A:VAL127 3.9 29.7 1.0
CD A:ARG131 3.9 19.3 0.6
C15 A:78W402 4.0 22.6 1.0
C9 A:78W402 4.0 39.6 1.0
NE A:ARG131 4.0 20.2 0.4
N A:THR128 4.0 14.0 1.0
C13 A:78W402 4.0 23.9 1.0
C A:VAL127 4.0 13.3 1.0
CD A:ARG131 4.1 18.9 0.4
CB A:THR128 4.1 18.1 0.5
CB A:ARG131 4.2 13.2 1.0
HG13 A:VAL127 4.2 29.7 1.0
HD22 A:LEU155 4.2 26.2 1.0
HG21 A:THR128 4.2 21.5 0.5
C3 A:78W402 4.2 31.8 1.0
OG1 A:THR128 4.2 14.9 0.5
HG1 A:THR128 4.3 17.9 0.5
HB A:THR128 4.3 21.7 0.5
H A:THR128 4.4 16.8 0.5
C14 A:78W402 4.5 22.1 1.0
H A:THR128 4.5 16.8 0.5
HG23 A:THR128 4.5 18.7 0.5
HB A:VAL127 4.6 24.3 1.0
CB A:THR128 4.6 14.5 0.5
HD13 A:LEU155 4.6 32.5 1.0
CB A:VAL127 4.7 20.2 1.0
CG A:ARG131 4.7 15.0 0.6
N8 A:78W402 4.7 39.8 1.0
CG A:ARG131 4.7 15.4 0.4
HZ A:PHE157 4.8 22.4 1.0
S21 A:78W402 4.8 43.0 1.0
HD2 A:ARG131 4.8 22.7 0.4
C2 A:78W402 4.9 33.8 1.0
H A:ARG131 4.9 13.3 1.0
C A:THR128 4.9 14.2 1.0

Chlorine binding site 3 out of 3 in 5lvo

Go back to Chlorine Binding Sites List in 5lvo
Chlorine binding site 3 out of 3 in the Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human PDK1 Kinase Domain in Complex with Allosteric Compound PSE10 Bound to the Pif-Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:51.2
occ:1.00
HB3 A:LYS123 3.1 29.2 1.0
HB2 A:TYR126 3.4 21.7 1.0
HG23 A:VAL127 3.7 25.7 1.0
HD12 A:ILE118 3.7 32.9 1.0
HG22 A:VAL127 3.9 25.7 1.0
HB3 A:TYR126 4.0 21.7 1.0
CB A:LYS123 4.0 24.3 1.0
CD A:LYS123 4.1 29.3 1.0
CB A:TYR126 4.1 18.1 1.0
HG3 A:LYS123 4.2 32.7 1.0
HD11 A:ILE118 4.2 32.9 1.0
CG2 A:VAL127 4.3 21.4 1.0
HD23 A:LEU113 4.3 30.6 1.0
CD1 A:ILE118 4.3 27.4 1.0
CG A:LYS123 4.3 27.2 1.0
HD21 A:LEU113 4.4 30.6 1.0
HD22 A:LEU113 4.4 30.6 1.0
HD13 A:ILE118 4.4 32.9 1.0
CB A:PHE93 4.4 32.0 1.0
HB2 A:LYS123 4.5 29.2 1.0
CD2 A:LEU113 4.6 25.5 1.0
O A:LYS123 4.6 18.2 1.0
HG21 A:VAL127 4.7 25.7 1.0
O A:HOH621 4.7 25.7 1.0
HD2 A:TYR126 4.7 31.4 1.0
H A:VAL127 4.8 18.0 1.0
N A:VAL127 4.9 15.0 1.0
CG A:TYR126 4.9 22.2 1.0
HA A:LYS123 5.0 26.2 1.0

Reference:

J.O.Schulze, G.Saladino, K.Busschots, S.Neimanis, E.Su, D.Odadzic, S.Zeuzem, V.Hindie, A.K.Herbrand, M.N.Lisa, P.M.Alzari, F.L.Gervasio, R.M.Biondi. Bidirectional Allosteric Communication Between the Atp-Binding Site and the Regulatory Pif Pocket in PDK1 Protein Kinase. Cell Chem Biol V. 23 1193 2016.
ISSN: ESSN 2451-9456
PubMed: 27693059
DOI: 10.1016/J.CHEMBIOL.2016.06.017
Page generated: Sat Jul 12 05:11:02 2025

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