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Chlorine in PDB 5l65: Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib

Enzymatic activity of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib

All present enzymatic activity of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib, PDB code: 5l65 was solved by M.Groll, E.M.Huber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.500, 300.390, 145.490, 90.00, 112.77, 90.00
R / Rfree (%) 17.6 / 20.1

Other elements in 5l65:

The structure of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib also contains other interesting chemical elements:

Magnesium (Mg) 7 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib (pdb code 5l65). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib, PDB code: 5l65:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5l65

Go back to Chlorine Binding Sites List in 5l65
Chlorine binding site 1 out of 4 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl302

b:40.8
occ:1.00
 OH H:TYR69 2.9 40.6 1.0
NH1 G:ARG111 3.0 42.2 1.0
OD1 G:ASN114 3.2 51.4 1.0
CD G:ARG111 3.7 41.3 1.0
CB G:ASN114 3.7 41.3 1.0
CE2 H:TYR69 3.8 42.9 1.0
CZ H:TYR69 3.8 42.5 1.0
CG G:ASN114 3.8 44.2 1.0
CZ G:ARG111 4.1 42.9 1.0
NE G:ARG111 4.3 43.2 1.0
CA G:ARG111 4.7 39.9 1.0
O G:ARG111 4.9 37.9 1.0
ND2 G:ASN114 5.0 44.2 1.0

Chlorine binding site 2 out of 4 in 5l65

Go back to Chlorine Binding Sites List in 5l65
Chlorine binding site 2 out of 4 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl203

b:60.8
occ:1.00
 NH2 N:ARG45 3.1 39.3 1.0
NE2 N:GLN53 3.2 38.0 1.0
NH1 N:ARG45 3.4 40.6 1.0
CG2 N:THR31 3.6 45.6 1.0
CZ N:ARG45 3.7 39.5 1.0
C46 N:3BV201 4.1 29.2 1.0
C45 N:3BV201 4.1 27.6 1.0
CB N:ALA49 4.1 38.5 1.0
OD1 H:ASP120 4.3 79.7 1.0
CD N:GLN53 4.3 36.9 1.0
CG N:GLN53 4.5 36.6 1.0
C44 N:3BV201 4.7 28.9 1.0
O H:THR119 4.7 46.2 1.0
CA N:ALA49 4.8 38.1 1.0
CB a:TYR228 4.8 46.9 1.0
O N:ASP32 4.8 46.6 1.0
OG1 N:THR20 4.9 47.3 1.0

Chlorine binding site 3 out of 4 in 5l65

Go back to Chlorine Binding Sites List in 5l65
Chlorine binding site 3 out of 4 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cl301

b:42.2
occ:1.00
 OH V:TYR69 3.0 43.9 1.0
NH1 U:ARG111 3.0 48.0 1.0
OD1 U:ASN114 3.2 52.5 1.0
CB U:ASN114 3.7 44.2 1.0
CD U:ARG111 3.7 43.8 1.0
CG U:ASN114 3.8 46.6 1.0
CZ V:TYR69 3.8 46.3 1.0
CE2 V:TYR69 3.8 47.0 1.0
CZ U:ARG111 4.1 47.4 1.0
NE U:ARG111 4.3 46.3 1.0
CA U:ARG111 4.7 42.2 1.0
O U:ARG111 4.8 42.7 1.0
ND2 U:ASN114 4.9 44.8 1.0
CG U:ARG111 5.0 42.2 1.0

Chlorine binding site 4 out of 4 in 5l65

Go back to Chlorine Binding Sites List in 5l65
Chlorine binding site 4 out of 4 in the Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Yeast 20S Proteasome with Mouse BETA5I (1-138) and Mouse BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cl202

b:57.0
occ:1.00
 NE2 b:GLN53 2.9 39.4 1.0
NH2 b:ARG45 3.2 42.1 1.0
NH1 b:ARG45 3.6 43.8 1.0
CG2 b:THR31 3.7 48.8 1.0
CZ b:ARG45 3.9 41.4 1.0
OD1 V:ASP120 4.1 77.0 1.0
CD b:GLN53 4.1 38.6 1.0
CB b:ALA49 4.1 41.0 1.0
C46 b:3BV201 4.3 30.5 1.0
C45 b:3BV201 4.4 29.4 1.0
O V:THR119 4.4 44.5 1.0
CG b:GLN53 4.4 39.1 1.0
CB M:TYR228 4.6 46.4 1.0
CA b:ALA49 4.8 40.8 1.0
C44 b:3BV201 4.9 30.5 1.0
OG1 b:THR20 4.9 47.1 1.0
O b:ASP32 5.0 48.4 1.0
O b:ALA49 5.0 38.9 1.0
CD2 M:TYR228 5.0 41.9 1.0

Reference:

E.M.Huber, W.Heinemeyer, G.De Bruin, H.S.Overkleeft, M.Groll. A Humanized Yeast Proteasome Identifies Unique Binding Modes of Inhibitors For the Immunosubunit Beta 5I. Embo J. V. 35 2602 2016.
ISSN: ESSN 1460-2075
PubMed: 27789522
DOI: 10.15252/EMBJ.201695222
Page generated: Fri Jul 26 11:10:19 2024

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