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Chlorine in PDB 6sbu: X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3)

Enzymatic activity of X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3)

All present enzymatic activity of X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3):
1.1.1.27;

Protein crystallography data

The structure of X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3), PDB code: 6sbu was solved by A.Friberg, V.Puetter, D.Nguyen, H.Rehwinkel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.80 / 2.91
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.445, 143.853, 311.225, 90.00, 90.00, 90.00
R / Rfree (%) 20.7 / 24.4

Chlorine Binding Sites:

The binding sites of Chlorine atom in the X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3) (pdb code 6sbu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3), PDB code: 6sbu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 6sbu

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Chlorine binding site 1 out of 8 in the X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1001

b:1.0
occ:1.00
 CLA A:L5N1001 0.0 1.0 1.0
CAV A:L5N1001 1.7 71.0 1.0
CAW A:L5N1001 2.7 67.8 1.0
SAR A:L5N1001 3.0 56.2 1.0
CD1 B:LEU173 3.5 54.3 1.0
OG B:SER237 3.6 97.7 1.0
CB B:SER237 3.8 84.0 1.0
CAS A:L5N1001 3.8 60.9 1.0
CG B:LEU173 3.9 50.3 1.0
O B:GLN233 4.0 71.6 1.0
CAO A:L5N1001 4.0 56.1 1.0
CD2 B:LEU173 4.1 52.0 1.0
CA B:VAL234 4.2 64.9 1.0
O B:ARG169 4.3 45.6 1.0
CB B:ARG169 4.3 47.2 1.0
C B:GLN233 4.4 68.1 1.0
N B:VAL234 4.5 63.2 1.0
CG B:ARG169 4.5 51.8 1.0
NE2 A:HIS67 4.6 45.5 1.0
CG2 B:VAL234 4.6 55.5 1.0
NE2 B:GLN233 4.7 77.0 1.0
C B:ARG169 4.8 42.1 1.0
CG B:GLN233 4.8 75.4 1.0
CA B:ARG169 4.9 42.2 1.0
CD B:ARG169 4.9 54.4 1.0
CD B:GLN233 4.9 80.6 1.0
O B:VAL234 5.0 78.4 1.0

Chlorine binding site 2 out of 8 in 6sbu

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Chlorine binding site 2 out of 8 in the X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1001

b:1.0
occ:1.00
 CLA B:L5N1001 0.0 1.0 1.0
CAV B:L5N1001 1.7 79.3 1.0
CAW B:L5N1001 2.8 72.0 1.0
SAR B:L5N1001 2.9 73.5 1.0
CB A:ARG169 3.4 56.7 1.0
O A:ARG169 3.5 54.6 1.0
CG A:ARG169 3.6 58.0 1.0
CD1 A:LEU173 3.7 41.3 1.0
C A:ARG169 3.9 57.1 1.0
CA A:ARG169 3.9 54.4 1.0
CAS B:L5N1001 3.9 67.6 1.0
CG A:LEU173 4.0 42.2 1.0
CA A:VAL234 4.0 71.8 1.0
CG2 A:VAL234 4.0 69.9 1.0
CAO B:L5N1001 4.1 70.2 1.0
CD A:ARG169 4.1 58.5 1.0
OG A:SER237 4.2 0.9 1.0
CB A:SER237 4.3 94.8 1.0
O A:GLN233 4.5 79.4 1.0
CD2 A:LEU173 4.5 42.8 1.0
CB A:VAL234 4.6 70.3 1.0
N A:VAL234 4.6 76.6 1.0
C A:GLN233 4.8 83.1 1.0
NE2 B:HIS67 4.8 68.9 1.0
N A:PHE170 4.8 52.9 1.0
O A:VAL234 4.9 79.1 1.0
NE A:ARG169 4.9 58.4 1.0

Chlorine binding site 3 out of 8 in 6sbu

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Chlorine binding site 3 out of 8 in the X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1001

b:0.3
occ:1.00
 CLA C:L5N1001 0.0 0.3 1.0
CAV C:L5N1001 1.7 74.5 1.0
CAW C:L5N1001 2.7 71.0 1.0
SAR C:L5N1001 3.0 65.0 1.0
OG D:SER237 3.6 92.7 1.0
CD1 D:LEU173 3.6 52.0 1.0
CB D:SER237 3.8 76.3 1.0
CAS C:L5N1001 3.8 68.9 1.0
CG D:LEU173 4.0 49.4 1.0
O D:GLN233 4.0 63.7 1.0
CAO C:L5N1001 4.1 65.1 1.0
CA D:VAL234 4.1 56.8 1.0
CB D:ARG169 4.1 46.5 1.0
O D:ARG169 4.2 45.3 1.0
CD2 D:LEU173 4.3 50.8 1.0
CG D:ARG169 4.3 49.6 1.0
C D:GLN233 4.4 60.9 1.0
N D:VAL234 4.4 58.1 1.0
CG2 D:VAL234 4.5 52.0 1.0
CD D:ARG169 4.6 50.9 1.0
NE2 C:HIS67 4.7 49.8 1.0
C D:ARG169 4.7 43.8 1.0
CA D:ARG169 4.7 43.3 1.0
O D:VAL234 4.8 66.4 1.0
CG D:GLN233 4.9 72.9 1.0
CB D:VAL234 4.9 54.5 1.0
C D:VAL234 5.0 59.1 1.0

Chlorine binding site 4 out of 8 in 6sbu

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Chlorine binding site 4 out of 8 in the X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl1001

b:0.1
occ:1.00
 CLA D:L5N1001 0.0 0.1 1.0
CAV D:L5N1001 1.7 73.2 1.0
CAW D:L5N1001 2.6 68.2 1.0
SAR D:L5N1001 3.0 63.4 1.0
OG C:SER237 3.5 91.0 1.0
CB C:SER237 3.7 86.9 1.0
CD1 C:LEU173 3.7 57.7 1.0
CAS D:L5N1001 3.8 69.0 1.0
CG C:LEU173 4.0 60.0 1.0
CAO D:L5N1001 4.0 64.7 1.0
O C:GLN233 4.1 64.9 1.0
CB C:ARG169 4.2 49.8 1.0
CA C:VAL234 4.2 55.6 1.0
CD2 C:LEU173 4.3 64.2 1.0
O C:ARG169 4.3 48.0 1.0
CG C:ARG169 4.3 51.7 1.0
NE2 D:HIS67 4.5 51.3 1.0
C C:GLN233 4.6 62.7 1.0
N C:VAL234 4.6 54.2 1.0
CG2 C:VAL234 4.6 56.8 1.0
CD C:ARG169 4.7 53.4 1.0
C C:ARG169 4.7 50.1 1.0
CA C:ARG169 4.8 49.0 1.0
NE2 C:GLN233 4.9 86.1 1.0
O C:VAL234 4.9 68.6 1.0

Chlorine binding site 5 out of 8 in 6sbu

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Chlorine binding site 5 out of 8 in the X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl1001

b:0.2
occ:1.00
 CLA E:L5N1001 0.0 0.2 1.0
CAV E:L5N1001 1.7 76.7 1.0
CAW E:L5N1001 2.7 75.7 1.0
SAR E:L5N1001 3.0 66.6 1.0
OG F:SER237 3.6 93.6 1.0
CD1 F:LEU173 3.6 55.9 1.0
CB F:SER237 3.8 83.8 1.0
CAS E:L5N1001 3.8 71.2 1.0
CG F:LEU173 3.9 54.4 1.0
CAO E:L5N1001 4.0 64.5 1.0
O F:GLN233 4.0 68.9 1.0
CB F:ARG169 4.1 55.5 1.0
CA F:VAL234 4.2 74.6 1.0
O F:ARG169 4.2 52.8 1.0
CD2 F:LEU173 4.2 53.7 1.0
CG F:ARG169 4.3 57.0 1.0
C F:GLN233 4.5 69.9 1.0
N F:VAL234 4.5 71.7 1.0
CG2 F:VAL234 4.5 66.6 1.0
NE2 E:HIS67 4.6 60.7 1.0
C F:ARG169 4.7 52.3 1.0
CD F:ARG169 4.7 60.0 1.0
CA F:ARG169 4.7 52.6 1.0
NE2 F:GLN233 4.9 80.3 1.0
O F:VAL234 4.9 86.6 1.0
CG F:GLN233 4.9 82.4 1.0
CB F:VAL234 4.9 71.3 1.0

Chlorine binding site 6 out of 8 in 6sbu

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Chlorine binding site 6 out of 8 in the X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl1001

b:0.8
occ:1.00
 CLA F:L5N1001 0.0 0.8 1.0
CAV F:L5N1001 1.7 95.8 1.0
CAW F:L5N1001 2.8 81.8 1.0
SAR F:L5N1001 2.9 85.7 1.0
CB E:ARG169 3.7 58.2 1.0
CD1 E:LEU173 3.8 71.3 1.0
OG E:SER237 3.8 0.3 1.0
CB E:SER237 3.8 0.3 1.0
CG E:ARG169 3.8 59.0 1.0
CAS F:L5N1001 3.9 78.7 1.0
O E:ARG169 3.9 55.5 1.0
CA E:VAL234 4.0 78.3 1.0
CAO F:L5N1001 4.0 81.2 1.0
CG E:LEU173 4.1 67.9 1.0
O E:GLN233 4.2 83.5 1.0
CD E:ARG169 4.2 59.9 1.0
CG2 E:VAL234 4.2 66.6 1.0
CA E:ARG169 4.3 58.2 1.0
C E:ARG169 4.3 58.1 1.0
N E:VAL234 4.5 81.5 1.0
NE2 F:HIS67 4.5 67.8 1.0
C E:GLN233 4.6 87.1 1.0
CD2 E:LEU173 4.6 63.5 1.0
O E:VAL234 4.6 85.9 1.0
CB E:VAL234 4.6 68.3 1.0
C E:VAL234 4.8 82.0 1.0
NE E:ARG169 4.9 56.4 1.0

Chlorine binding site 7 out of 8 in 6sbu

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Chlorine binding site 7 out of 8 in the X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Cl1001

b:0.9
occ:1.00
 CLA G:L5N1001 0.0 0.9 1.0
CAV G:L5N1001 1.7 81.7 1.0
CAW G:L5N1001 2.7 74.4 1.0
SAR G:L5N1001 3.0 71.7 1.0
CD1 H:LEU173 3.6 50.6 1.0
OG H:SER237 3.6 84.5 1.0
CAS G:L5N1001 3.8 71.7 1.0
CB H:SER237 3.8 77.0 1.0
CG H:LEU173 3.9 50.5 1.0
O H:GLN233 4.0 60.7 1.0
CAO G:L5N1001 4.0 68.0 1.0
CB H:ARG169 4.1 62.8 1.0
CA H:VAL234 4.1 58.7 1.0
O H:ARG169 4.1 52.2 1.0
CG H:ARG169 4.3 62.1 1.0
CD2 H:LEU173 4.3 48.0 1.0
C H:GLN233 4.5 60.5 1.0
N H:VAL234 4.5 58.7 1.0
CG2 H:VAL234 4.5 64.2 1.0
C H:ARG169 4.6 55.1 1.0
CA H:ARG169 4.7 57.9 1.0
CD H:ARG169 4.7 65.6 1.0
NE2 G:HIS67 4.7 54.5 1.0
O H:VAL234 4.9 70.6 1.0
CB H:VAL234 4.9 57.7 1.0
CG H:GLN233 4.9 75.7 1.0

Chlorine binding site 8 out of 8 in 6sbu

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Chlorine binding site 8 out of 8 in the X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of X-Ray Structure of Human Ldha with An Allosteric Inhibitor (Compound 3) within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Cl1001

b:0.6
occ:1.00
 CLA H:L5N1001 0.0 0.6 1.0
CAV H:L5N1001 1.7 80.4 1.0
CAW H:L5N1001 2.7 72.6 1.0
SAR H:L5N1001 3.0 64.3 1.0
OG G:SER237 3.7 87.2 1.0
CD1 G:LEU173 3.7 60.3 1.0
CB G:SER237 3.7 78.3 1.0
CA G:VAL234 3.8 58.0 1.0
CB G:ARG169 3.9 59.8 1.0
CAS H:L5N1001 3.9 65.9 1.0
O G:GLN233 4.0 69.3 1.0
CG G:ARG169 4.0 61.0 1.0
O G:ARG169 4.1 59.3 1.0
CG G:LEU173 4.1 63.7 1.0
CAO H:L5N1001 4.1 66.3 1.0
CG2 G:VAL234 4.2 59.2 1.0
N G:VAL234 4.3 58.3 1.0
C G:GLN233 4.4 68.5 1.0
CD G:ARG169 4.4 64.1 1.0
C G:ARG169 4.5 57.3 1.0
CA G:ARG169 4.5 58.1 1.0
CD2 G:LEU173 4.5 63.0 1.0
O G:VAL234 4.6 71.2 1.0
CB G:VAL234 4.6 59.5 1.0
NE2 H:HIS67 4.7 52.1 1.0
C G:VAL234 4.7 61.9 1.0
NE G:ARG169 5.0 64.0 1.0

Reference:

A.Friberg, H.Rehwinkel, D.Nguyen, V.Puetter, M.Quanz, J.Weiske, U.Eberspaecher, I.Heisler, G.Langer. Structural Evidence For Isoform-Selective Allosteric Inhibition of Lactate Dehydrogenase A Acs Omega 2020.
ISSN: ESSN 2470-1343
DOI: 10.1021/ACSOMEGA.0C00715
Page generated: Mon Jul 29 14:53:50 2024

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