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Chlorine in PDB 5l5y: Yeast 20S Proteasome with Human BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Carfilzomib

Enzymatic activity of Yeast 20S Proteasome with Human BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Carfilzomib

All present enzymatic activity of Yeast 20S Proteasome with Human BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Carfilzomib:
3.4.25.1;

Protein crystallography data

The structure of Yeast 20S Proteasome with Human BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Carfilzomib, PDB code: 5l5y 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 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 135.970, 299.890, 145.570, 90.00, 112.57, 90.00
R / Rfree (%) 18.6 / 20.7

Other elements in 5l5y:

The structure of Yeast 20S Proteasome with Human BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Carfilzomib also contains other interesting chemical elements:

Magnesium (Mg) 10 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Yeast 20S Proteasome with Human BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Carfilzomib (pdb code 5l5y). 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 Human BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Carfilzomib, PDB code: 5l5y:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5l5y

Go back to Chlorine Binding Sites List in 5l5y
Chlorine binding site 1 out of 4 in the Yeast 20S Proteasome with Human BETA5C (1-138) and Human 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 Human BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl302

b:44.9
occ:1.00
 OH H:TYR69 2.9 42.4 1.0
NH1 G:ARG111 3.0 38.4 1.0
OD1 G:ASN114 3.2 42.0 1.0
CD G:ARG111 3.7 37.9 1.0
CZ H:TYR69 3.7 41.1 1.0
CE2 H:TYR69 3.7 40.7 1.0
CB G:ASN114 3.8 38.8 1.0
CG G:ASN114 3.9 39.5 1.0
O H:HOH422 3.9 57.3 1.0
CZ G:ARG111 4.1 38.2 1.0
NE G:ARG111 4.3 38.8 1.0
CA G:ARG111 4.7 38.5 1.0
O G:ARG111 4.8 38.0 1.0
CE1 H:TYR69 5.0 41.1 1.0
CG G:ARG111 5.0 37.6 1.0

Chlorine binding site 2 out of 4 in 5l5y

Go back to Chlorine Binding Sites List in 5l5y
Chlorine binding site 2 out of 4 in the Yeast 20S Proteasome with Human BETA5C (1-138) and Human 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 Human BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Cl203

b:57.1
occ:1.00
 NH2 N:ARG45 3.1 36.4 1.0
NE2 N:GLN53 3.2 33.2 1.0
NH1 N:ARG45 3.4 35.9 1.0
CG2 N:THR31 3.6 42.5 1.0
CZ N:ARG45 3.7 36.1 1.0
C46 N:3BV201 4.1 41.7 1.0
C45 N:3BV201 4.1 40.6 1.0
CB N:ALA49 4.2 32.3 1.0
OD1 H:ASP120 4.2 74.7 1.0
CD N:GLN53 4.3 33.7 1.0
C44 N:3BV201 4.5 41.1 1.0
CG N:GLN53 4.6 32.5 1.0
O H:THR119 4.6 42.0 1.0
CA N:ALA49 4.8 32.9 1.0
CB a:TYR228 4.8 47.2 1.0
O N:ASP32 4.9 41.1 1.0
O N:ALA49 5.0 33.2 1.0

Chlorine binding site 3 out of 4 in 5l5y

Go back to Chlorine Binding Sites List in 5l5y
Chlorine binding site 3 out of 4 in the Yeast 20S Proteasome with Human BETA5C (1-138) and Human 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 Human BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Cl301

b:45.9
occ:1.00
 OH V:TYR69 2.9 43.9 1.0
NH1 U:ARG111 3.0 44.8 1.0
OD1 U:ASN114 3.2 44.2 1.0
CD U:ARG111 3.7 39.9 1.0
CB U:ASN114 3.7 40.1 1.0
CZ V:TYR69 3.7 41.7 1.0
CE2 V:TYR69 3.7 41.5 1.0
CG U:ASN114 3.8 41.4 1.0
CZ U:ARG111 4.1 43.4 1.0
NE U:ARG111 4.3 42.2 1.0
CA U:ARG111 4.7 37.2 1.0
O U:ARG111 4.8 38.8 1.0
CG U:ARG111 5.0 38.3 1.0
CE1 V:TYR69 5.0 41.4 1.0

Chlorine binding site 4 out of 4 in 5l5y

Go back to Chlorine Binding Sites List in 5l5y
Chlorine binding site 4 out of 4 in the Yeast 20S Proteasome with Human BETA5C (1-138) and Human 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 Human BETA5C (1-138) and Human BETA6 (97- 111; 118-133) in Complex with Carfilzomib within 5.0Å range:
probe atom residue distance (Å) B Occ
b:Cl203

b:51.6
occ:1.00
 NE2 b:GLN53 3.1 32.9 1.0
NH2 b:ARG45 3.1 35.2 1.0
NH1 b:ARG45 3.4 36.0 1.0
CZ b:ARG45 3.7 34.9 1.0
CG2 b:THR31 3.7 42.5 1.0
CB b:ALA49 4.1 33.4 1.0
C45 b:3BV201 4.2 41.5 1.0
OD1 V:ASP120 4.2 72.7 1.0
CD b:GLN53 4.2 32.5 1.0
C46 b:3BV201 4.4 42.2 1.0
CG b:GLN53 4.5 32.7 1.0
O V:THR119 4.5 42.8 1.0
CB M:TYR228 4.7 47.1 1.0
CA b:ALA49 4.7 34.0 1.0
C44 b:3BV201 4.7 41.7 1.0
O b:ALA49 4.9 34.2 1.0
O b:ASP32 5.0 40.9 1.0
CD2 M:TYR228 5.0 43.3 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: Sat Dec 12 12:00:13 2020

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