Chlorine in PDB 8pkx: Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec)

Protein crystallography data

The structure of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec), PDB code: 8pkx was solved by M.B.Braun, L.Bischof, M.D.Hartmann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.24 / 1.79
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.43, 68.877, 78.252, 90, 117.68, 90
R / Rfree (%) 17.5 / 21

Other elements in 8pkx:

The structure of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec) also contains other interesting chemical elements:

Sodium (Na) 4 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec) (pdb code 8pkx). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec), PDB code: 8pkx:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in 8pkx

Go back to Chlorine Binding Sites List in 8pkx
Chlorine binding site 1 out of 2 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:80.4
occ:1.00
NH2 A:ARG354 3.6 42.7 1.0
NH1 A:ARG354 3.9 43.4 1.0
O A:HOH845 4.0 56.9 1.0
O2 A:EDO703 4.2 75.2 1.0
CZ A:ARG354 4.2 44.1 1.0
CE1 A:TYR341 4.5 55.9 1.0

Chlorine binding site 2 out of 2 in 8pkx

Go back to Chlorine Binding Sites List in 8pkx
Chlorine binding site 2 out of 2 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 11 (Ortho-Wrcdeetgec) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl702

b:64.2
occ:1.00
O A:HOH897 2.6 50.2 1.0
O A:HOH958 2.8 32.9 1.0
N A:GLY367 2.9 27.6 1.0
NA A:NA711 3.0 61.2 1.0
N A:VAL606 3.1 29.6 0.7
N A:VAL606 3.1 29.9 0.3
O A:VAL606 3.4 31.7 0.7
O A:VAL606 3.5 25.1 0.3
CA A:GLY605 3.5 29.9 1.0
O A:GLY367 3.6 31.0 1.0
O A:HOH974 3.6 54.2 1.0
CA A:ALA366 3.6 27.8 1.0
C A:ALA366 3.8 28.1 1.0
C A:GLY605 3.8 30.9 1.0
CA A:GLY367 3.9 28.9 1.0
CG2 A:VAL606 4.0 27.3 0.3
CB A:ALA366 4.0 28.7 1.0
CA A:VAL606 4.1 30.5 0.7
CA A:VAL606 4.2 28.9 0.3
C A:VAL606 4.2 30.2 0.7
C A:GLY367 4.2 32.1 1.0
C A:VAL606 4.2 28.0 0.3
O A:HOH956 4.3 30.2 1.0
O A:HOH930 4.4 44.2 1.0
O A:VAL604 4.4 30.5 1.0
CB A:VAL606 4.5 25.4 0.7
CB A:VAL606 4.7 28.9 0.3
N A:GLY605 4.7 29.1 1.0
O A:LEU365 4.7 31.8 1.0
N A:ALA366 4.9 27.6 1.0
O A:ILE559 4.9 30.4 1.0
O A:ALA366 5.0 28.4 1.0
CG2 A:VAL606 5.0 30.4 0.7
C A:VAL604 5.0 32.1 1.0

Reference:

F.Fonseca Lopez, J.Miao, J.Damjanovic, L.Bischof, M.B.Braun, Y.Ling, M.D.Hartmann, Y.S.Lin, J.A.Kritzer. Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of KEAP1 Binders. J.Chem.Inf.Model. 2023.
ISSN: ESSN 1549-960X
PubMed: 37917529
DOI: 10.1021/ACS.JCIM.3C01337
Page generated: Tue Jul 30 11:38:01 2024

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