Chlorine in PDB 8pkv: Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec)

Protein crystallography data

The structure of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec), PDB code: 8pkv 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) 42.19 / 1.55
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 162.957, 68.861, 77.95, 90, 117.66, 90
R / Rfree (%) 15.7 / 19.2

Other elements in 8pkv:

The structure of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec) also contains other interesting chemical elements:

Sodium (Na) 8 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 4 (Ortho-Wrcdeetgec) (pdb code 8pkv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec), PDB code: 8pkv:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 8pkv

Go back to Chlorine Binding Sites List in 8pkv
Chlorine binding site 1 out of 3 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (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 4 (Ortho-Wrcdeetgec) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl704

b:87.1
occ:1.00
NE A:ARG326 3.2 51.7 0.5
N A:GLN563 3.3 31.4 1.0
NH1 A:ARG326 3.7 58.8 0.5
CD A:ARG326 4.0 48.4 0.5
CG A:GLN563 4.0 46.9 1.0
NH2 A:ARG326 4.0 52.7 0.5
CZ A:ARG326 4.0 53.3 0.5
CA A:GLN563 4.1 34.6 1.0
CA A:HIS562 4.1 28.5 1.0
CD2 A:HIS562 4.2 39.3 1.0
C A:HIS562 4.2 29.9 1.0
O A:HOH945 4.3 41.6 1.0
CD A:ARG326 4.4 45.9 0.5
CG1 A:VAL608 4.4 30.3 1.0
CG A:HIS562 4.5 34.3 1.0
CB A:GLN563 4.6 37.7 1.0
NE2 A:HIS562 4.7 38.7 1.0
CZ A:ARG326 4.8 54.9 0.5
CB A:ARG326 4.8 39.8 0.5
CB A:ARG326 4.8 37.7 0.5
CG A:ARG326 4.9 40.0 0.5
CB A:HIS562 4.9 30.0 1.0
O A:VAL561 4.9 28.3 1.0
CG A:ARG326 5.0 43.4 0.5

Chlorine binding site 2 out of 3 in 8pkv

Go back to Chlorine Binding Sites List in 8pkv
Chlorine binding site 2 out of 3 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (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 4 (Ortho-Wrcdeetgec) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl705

b:57.8
occ:1.00
O A:HOH998 2.7 33.9 1.0
O A:HOH934 2.7 38.9 1.0
N A:GLY367 3.0 25.6 1.0
N A:VAL606 3.0 24.0 0.5
N A:VAL606 3.0 25.7 0.5
NA A:NA717 3.1 47.9 1.0
CA A:GLY605 3.4 24.2 1.0
O A:VAL606 3.4 24.5 0.5
O A:VAL606 3.5 24.6 0.5
CA A:ALA366 3.7 24.0 1.0
O A:GLY367 3.7 28.2 1.0
C A:GLY605 3.7 25.4 1.0
O A:HOH1024 3.8 44.4 1.0
C A:ALA366 3.8 23.0 1.0
CA A:GLY367 3.9 23.9 1.0
CA A:VAL606 4.1 22.2 0.5
CG1 A:VAL606 4.1 29.3 0.5
CB A:ALA366 4.1 25.0 1.0
CA A:VAL606 4.1 27.2 0.5
C A:VAL606 4.2 22.8 0.5
O A:VAL604 4.2 27.0 1.0
C A:VAL606 4.2 24.2 0.5
C A:GLY367 4.2 25.4 1.0
O A:HOH931 4.3 34.9 1.0
O A:HOH984 4.4 30.0 1.0
CB A:VAL606 4.5 21.9 0.5
N A:GLY605 4.6 23.7 1.0
O A:LEU365 4.6 25.9 1.0
CB A:VAL606 4.8 29.9 0.5
C A:VAL604 4.8 25.5 1.0
CG2 A:VAL606 4.9 21.8 0.5
O A:ILE559 4.9 27.2 1.0
N A:ALA366 4.9 23.4 1.0
O A:GLY605 4.9 29.2 1.0

Chlorine binding site 3 out of 3 in 8pkv

Go back to Chlorine Binding Sites List in 8pkv
Chlorine binding site 3 out of 3 in the Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Kelch Domain of KEAP1 in Complex with A Ortho-Dimethylbenzene Linked Cyclic Peptide 4 (Ortho-Wrcdeetgec) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl706

b:65.2
occ:1.00
O A:HOH876 2.4 47.7 1.0
OD1 A:ASN438 3.0 36.2 1.0
O A:HOH1021 3.1 57.7 1.0
N A:ASN438 3.1 29.4 1.0
N A:SER439 3.2 28.0 1.0
CA A:HIS437 3.4 29.6 1.0
OG A:SER439 3.6 30.9 1.0
CB A:SER439 3.6 30.3 1.0
O A:HOH844 3.6 39.7 1.0
ND1 A:HIS437 3.7 30.5 1.0
NH1 A:ARG459 3.7 50.7 1.0
C A:HIS437 3.8 29.3 1.0
O A:HOH898 3.8 50.6 1.0
CB A:HIS437 3.8 29.0 1.0
CG A:ASN438 4.0 35.1 1.0
CA A:SER439 4.0 29.9 1.0
C A:ASN438 4.0 29.8 1.0
CA A:ASN438 4.0 29.2 1.0
O A:HOH1032 4.1 65.1 1.0
CG A:HIS437 4.2 27.2 1.0
O A:HIS436 4.5 32.0 0.3
O A:HIS436 4.5 33.5 0.7
N A:HIS437 4.6 28.8 1.0
CB A:ASN438 4.6 33.0 1.0
CZ A:ARG459 4.8 51.1 1.0
CE1 A:HIS437 4.9 30.3 1.0
ND2 A:ASN438 4.9 37.0 1.0
C A:HIS436 4.9 31.4 0.3
C A:HIS436 5.0 33.0 0.7
O A:HIS437 5.0 29.6 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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy