Atomistry » Arsenic » PDB 5yvb-6i5n » 6fmi
Atomistry »
  Arsenic »
    PDB 5yvb-6i5n »
      6fmi »

Arsenic in PDB 6fmi: Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2)

Protein crystallography data

The structure of Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2), PDB code: 6fmi was solved by P.Soares, X.Lucas, A.Ciulli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.18 / 2.80
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 63.972, 69.863, 356.939, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 25.6

Arsenic Binding Sites:

The binding sites of Arsenic atom in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2) (pdb code 6fmi). This binding sites where shown within 5.0 Angstroms radius around Arsenic atom.
In total 6 binding sites of Arsenic where determined in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2), PDB code: 6fmi:
Jump to Arsenic binding site number: 1; 2; 3; 4; 5; 6;

Arsenic binding site 1 out of 6 in 6fmi

Go back to Arsenic Binding Sites List in 6fmi
Arsenic binding site 1 out of 6 in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 1 of Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As60

b:75.0
occ:1.00
 AS A:CAS60 0.0 75.0 1.0
CE1 A:CAS60 2.0 76.4 1.0
CE2 A:CAS60 2.0 72.2 1.0
SG A:CAS60 2.2 61.7 1.0
CB A:CAS60 3.2 55.2 1.0
CA A:CAS60 3.5 51.4 1.0
CD2 A:LEU51 4.2 50.2 1.0
N A:CAS60 4.3 48.9 1.0
NE2 A:GLN49 4.6 66.6 1.0
O A:GLU59 4.7 52.0 1.0
C A:GLU59 4.7 52.4 1.0
C A:CAS60 4.7 50.3 1.0
CG A:LYS55 4.8 54.5 1.0
CD A:GLN49 4.9 63.9 1.0
O A:HOH226 4.9 59.5 1.0
CD A:LYS55 4.9 56.9 1.0
O A:CAS60 4.9 47.2 1.0

Arsenic binding site 2 out of 6 in 6fmi

Go back to Arsenic Binding Sites List in 6fmi
Arsenic binding site 2 out of 6 in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 2 of Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:As89

b:0.1
occ:1.00
 AS A:CAS89 0.0 0.1 1.0
CE2 A:CAS89 2.0 99.1 1.0
CE1 A:CAS89 2.0 0.9 1.0
SG A:CAS89 2.2 89.0 1.0
CB A:CAS89 3.1 81.7 1.0
CA A:CAS89 3.5 72.6 1.0
N A:ILE90 3.8 60.6 1.0
C A:CAS89 3.9 63.6 1.0
C A:ILE90 4.5 57.5 1.0
O A:ILE90 4.6 58.3 1.0
CA A:ILE90 4.8 57.5 1.0
N A:GLU91 4.9 56.4 1.0
N A:CAS89 4.9 70.2 1.0
O A:CAS89 4.9 62.2 1.0
OE2 A:GLU91 4.9 73.2 1.0

Arsenic binding site 3 out of 6 in 6fmi

Go back to Arsenic Binding Sites List in 6fmi
Arsenic binding site 3 out of 6 in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 3 of Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:As77

b:63.2
occ:1.00
 AS C:CAS77 0.0 63.2 1.0
CE1 C:CAS77 2.0 60.8 1.0
CE2 C:CAS77 2.0 63.8 1.0
SG C:CAS77 2.2 54.7 1.0
CB C:CAS77 3.2 46.1 1.0
CA C:CAS77 3.6 42.0 1.0
CA C:GLY106 4.1 42.0 1.0
O C:THR105 4.1 38.4 1.0
C C:CAS77 4.3 39.7 1.0
N C:GLY106 4.3 42.8 1.0
C C:THR105 4.4 41.3 1.0
N C:ASN78 4.4 39.1 1.0
N C:CAS77 4.8 40.4 1.0
NH2 C:ARG79 4.9 57.2 1.0
CZ C:ARG79 4.9 55.0 1.0
CE2 C:PHE148 5.0 44.3 1.0

Arsenic binding site 4 out of 6 in 6fmi

Go back to Arsenic Binding Sites List in 6fmi
Arsenic binding site 4 out of 6 in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 4 of Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As60

b:0.1
occ:1.00
 AS D:CAS60 0.0 0.1 1.0
CE2 D:CAS60 2.0 0.6 1.0
CE1 D:CAS60 2.0 0.9 1.0
SG D:CAS60 2.2 98.3 1.0
CB D:CAS60 3.2 89.6 1.0
CA D:CAS60 3.5 87.1 1.0
N D:CAS60 4.2 86.7 1.0
CD2 D:LEU51 4.2 89.9 1.0
O D:GLU59 4.6 90.1 1.0
C D:GLU59 4.6 88.5 1.0
NE2 D:GLN49 4.7 90.9 1.0
C D:CAS60 4.8 84.0 1.0

Arsenic binding site 5 out of 6 in 6fmi

Go back to Arsenic Binding Sites List in 6fmi
Arsenic binding site 5 out of 6 in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 5 of Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:As89

b:1.0
occ:1.00
 AS D:CAS89 0.0 1.0 1.0
CE1 D:CAS89 2.0 1.0 1.0
CE2 D:CAS89 2.0 0.5 1.0
SG D:CAS89 2.2 0.5 1.0
CB D:CAS89 3.1 0.2 1.0
CA D:CAS89 3.5 0.3 1.0
N D:ILE90 3.6 0.3 1.0
C D:CAS89 3.8 0.3 1.0
O D:ILE90 3.9 1.0 1.0
C D:ILE90 4.1 0.3 1.0
OE2 D:GLU91 4.2 0.9 1.0
CA D:ILE90 4.5 0.6 1.0
N D:GLU91 4.7 99.5 1.0
O D:CAS89 4.8 0.9 1.0
N D:CAS89 4.9 0.1 1.0
CD D:GLU91 5.0 0.5 1.0

Arsenic binding site 6 out of 6 in 6fmi

Go back to Arsenic Binding Sites List in 6fmi
Arsenic binding site 6 out of 6 in the Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2)


Mono view


Stereo pair view

A full contact list of Arsenic with other atoms in the As binding site number 6 of Pvhl:Elob:Eloc in Complex with N-((S)-1-((2S,4R)-4-Hydroxy-2-((4-(4- Methylthiazol-5-Yl)Benzyl)Carbamothioyl) Pyrrolidin-1-Yl)-1- Oxopropan-2-Yl)Acetamide (Ligand 2) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:As77

b:74.4
occ:1.00
 AS F:CAS77 0.0 74.4 1.0
CE2 F:CAS77 2.0 75.5 1.0
CE1 F:CAS77 2.0 76.5 1.0
SG F:CAS77 2.2 66.2 1.0
CB F:CAS77 3.1 57.5 1.0
CA F:CAS77 3.5 52.5 1.0
CA F:GLY106 4.0 47.3 1.0
N F:GLY106 4.2 47.4 1.0
C F:CAS77 4.3 49.1 1.0
N F:ASN78 4.4 47.4 1.0
O F:THR105 4.4 44.3 1.0
C F:THR105 4.4 46.0 1.0
N F:CAS77 4.8 51.4 1.0
O F:PHE76 4.9 51.9 1.0

Reference:

P.Soares, X.Lucas, A.Ciulli. Thioamide Substitution to Probe the Hydroxyproline Recognition of Vhl Ligands. Bioorg. Med. Chem. V. 26 2992 2018.
ISSN: ESSN 1464-3391
PubMed: 29650462
DOI: 10.1016/J.BMC.2018.03.034
Page generated: Wed Jul 10 13:17:14 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy