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Fluorine in PDB 7fqk: Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide

Enzymatic activity of Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide

All present enzymatic activity of Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide:
3.4.22.34;

Protein crystallography data

The structure of Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide, PDB code: 7fqk was solved by A.Ehler, J.Benz, B.Bartels, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 87.13 / 1.97
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 102.489, 102.489, 330.991, 90, 90, 90
R / Rfree (%) 19.4 / 23.3

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide (pdb code 7fqk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide, PDB code: 7fqk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 12 in 7fqk

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Fluorine binding site 1 out of 12 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:46.4
occ:1.00
 F16 A:WS9502 0.0 46.4 1.0
C15 A:WS9502 1.4 52.8 1.0
F17 A:WS9502 2.3 49.8 1.0
F18 A:WS9502 2.4 47.5 1.0
O14 A:WS9502 2.4 43.1 1.0
C11 A:WS9502 3.0 39.7 1.0
O A:HOH702 3.1 50.0 1.0
C10 A:WS9502 3.3 38.3 1.0
CD2 A:TYR228 3.7 34.5 1.0
O A:TYR41 3.8 57.5 1.0
CE2 A:TYR228 3.9 35.3 1.0
C12 A:WS9502 4.0 36.7 1.0
CB A:TYR41 4.2 62.2 1.0
CA A:TYR41 4.4 58.7 1.0
C9 A:WS9502 4.4 34.5 1.0
C A:TYR41 4.5 56.2 1.0
CG A:TYR41 4.6 67.7 1.0
CD1 A:TYR41 4.7 70.4 1.0
NH1 A:ARG44 4.7 53.9 1.0
OG1 A:THR227 4.7 35.3 1.0
N A:TYR228 4.8 33.7 1.0
CG A:TYR228 4.9 34.1 1.0
CA A:THR227 4.9 34.5 1.0

Fluorine binding site 2 out of 12 in 7fqk

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Fluorine binding site 2 out of 12 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:49.8
occ:1.00
 F17 A:WS9502 0.0 49.8 1.0
C15 A:WS9502 1.4 52.8 1.0
O14 A:WS9502 2.1 43.1 1.0
F18 A:WS9502 2.2 47.5 1.0
F16 A:WS9502 2.3 46.4 1.0
CG A:TYR41 3.1 67.7 1.0
CB A:TYR41 3.2 62.2 1.0
C11 A:WS9502 3.4 39.7 1.0
O D:HOH669 3.4 33.3 1.0
CD2 A:TYR41 3.4 71.5 1.0
CD1 A:TYR41 3.6 70.4 1.0
O A:HOH702 3.7 50.0 1.0
CA A:TYR41 4.1 58.7 1.0
CE2 A:TYR41 4.2 73.8 1.0
C10 A:WS9502 4.2 38.3 1.0
C12 A:WS9502 4.3 36.7 1.0
CE1 A:TYR41 4.3 73.0 1.0
O A:TYR41 4.4 57.5 1.0
O A:HOH686 4.5 32.6 1.0
CZ A:TYR41 4.6 75.5 1.0
C A:TYR41 4.7 56.2 1.0

Fluorine binding site 3 out of 12 in 7fqk

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Fluorine binding site 3 out of 12 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:47.5
occ:1.00
 F18 A:WS9502 0.0 47.5 1.0
C15 A:WS9502 1.4 52.8 1.0
O14 A:WS9502 2.1 43.1 1.0
F17 A:WS9502 2.2 49.8 1.0
F16 A:WS9502 2.4 46.4 1.0
C11 A:WS9502 2.7 39.7 1.0
C12 A:WS9502 3.0 36.7 1.0
O A:HOH702 3.4 50.0 1.0
C10 A:WS9502 3.8 38.3 1.0
O D:HOH669 3.9 33.3 1.0
C13 A:WS9502 4.2 34.0 1.0
CE2 A:TYR228 4.6 35.3 1.0
C9 A:WS9502 4.8 34.5 1.0
O D:HOH695 4.9 24.4 1.0
C8 A:WS9502 5.0 33.5 1.0

Fluorine binding site 4 out of 12 in 7fqk

Go back to Fluorine Binding Sites List in 7fqk
Fluorine binding site 4 out of 12 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:34.4
occ:1.00
 F16 B:WS9502 0.0 34.4 1.0
C15 B:WS9502 1.4 35.6 1.0
O14 B:WS9502 2.2 30.6 1.0
F17 B:WS9502 2.2 34.5 1.0
F18 B:WS9502 2.2 35.4 1.0
C11 B:WS9502 2.7 28.7 1.0
C10 B:WS9502 2.7 26.5 1.0
O B:HOH646 2.9 22.9 1.0
O B:HOH610 3.0 25.6 1.0
O B:TYR41 3.2 35.1 1.0
NH1 B:ARG44 3.7 35.0 1.0
CB B:TYR41 3.7 36.3 1.0
C B:TYR41 3.9 35.3 1.0
C12 B:WS9502 3.9 28.1 1.0
C9 B:WS9502 4.0 26.2 1.0
CA B:TYR41 4.0 35.8 1.0
CG B:TYR41 4.4 36.9 1.0
CZ B:ARG44 4.6 35.1 1.0
O C:HOH657 4.7 30.0 1.0
CD2 B:TYR228 4.7 35.9 1.0
NH2 B:ARG44 4.8 35.7 1.0
N33 C:WS9501 4.8 40.7 1.0
C13 B:WS9502 4.9 29.5 1.0
CD1 B:TYR41 4.9 36.9 1.0
C8 B:WS9502 5.0 26.6 1.0

Fluorine binding site 5 out of 12 in 7fqk

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Fluorine binding site 5 out of 12 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:34.5
occ:1.00
 F17 B:WS9502 0.0 34.5 1.0
C15 B:WS9502 1.3 35.6 1.0
O14 B:WS9502 2.2 30.6 1.0
F16 B:WS9502 2.2 34.4 1.0
F18 B:WS9502 2.2 35.4 1.0
OG C:SER215 3.0 37.1 1.0
O C:HOH657 3.2 30.0 1.0
CG B:TYR41 3.4 36.9 1.0
CB B:TYR41 3.5 36.3 1.0
C11 B:WS9502 3.5 28.7 1.0
CD1 B:TYR41 3.7 36.9 1.0
CD2 B:TYR41 3.7 37.6 1.0
O B:HOH646 4.0 22.9 1.0
C5 C:WS9501 4.2 26.9 1.0
C10 B:WS9502 4.3 26.5 1.0
CA B:TYR41 4.3 35.8 1.0
CB C:SER215 4.3 36.6 1.0
CE2 B:TYR41 4.3 38.2 1.0
CE1 B:TYR41 4.4 37.6 1.0
C12 B:WS9502 4.4 28.1 1.0
C4 C:WS9501 4.4 26.4 1.0
N33 C:WS9501 4.5 40.7 1.0
O B:HOH610 4.5 25.6 1.0
CZ B:TYR41 4.6 38.2 1.0
O B:TYR41 4.7 35.1 1.0
C B:TYR41 4.9 35.3 1.0

Fluorine binding site 6 out of 12 in 7fqk

Go back to Fluorine Binding Sites List in 7fqk
Fluorine binding site 6 out of 12 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:35.4
occ:1.00
 F18 B:WS9502 0.0 35.4 1.0
C15 B:WS9502 1.4 35.6 1.0
O14 B:WS9502 2.2 30.6 1.0
F17 B:WS9502 2.2 34.5 1.0
F16 B:WS9502 2.2 34.4 1.0
C11 B:WS9502 2.8 28.7 1.0
C4 C:WS9501 2.9 26.4 1.0
O B:HOH646 2.9 22.9 1.0
C5 C:WS9501 3.3 26.9 1.0
C12 B:WS9502 3.4 28.1 1.0
C10 B:WS9502 3.6 26.5 1.0
CE2 B:TYR228 4.0 36.2 1.0
CD2 B:TYR228 4.1 35.9 1.0
C3 C:WS9501 4.3 26.1 1.0
OG C:SER215 4.5 37.1 1.0
C13 B:WS9502 4.5 29.5 1.0
C9 B:WS9502 4.7 26.2 1.0
C1 C:WS9501 4.7 27.8 1.0
O B:TYR41 4.8 35.1 1.0
N33 C:WS9501 4.9 40.7 1.0
CB B:TYR41 4.9 36.3 1.0

Fluorine binding site 7 out of 12 in 7fqk

Go back to Fluorine Binding Sites List in 7fqk
Fluorine binding site 7 out of 12 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:43.5
occ:1.00
 F16 C:WS9501 0.0 43.5 1.0
C15 C:WS9501 1.4 45.9 1.0
F18 C:WS9501 2.3 42.6 1.0
F17 C:WS9501 2.3 40.5 1.0
O14 C:WS9501 2.4 36.0 1.0
C11 C:WS9501 3.1 34.4 1.0
C10 C:WS9501 3.4 32.4 1.0
O C:TYR41 3.4 52.2 1.0
O C:HOH644 3.5 25.2 1.0
CD2 C:TYR228 3.6 34.8 1.0
CE2 C:TYR228 4.0 35.0 1.0
C12 C:WS9501 4.1 32.6 1.0
CB C:TYR41 4.1 60.5 1.0
CA C:TYR41 4.1 55.6 1.0
C C:TYR41 4.2 51.3 1.0
OG1 C:THR227 4.5 34.8 1.0
NH1 C:ARG44 4.5 43.9 1.0
C9 C:WS9501 4.5 33.1 1.0
CG C:TYR41 4.6 66.5 1.0
O C:HOH625 4.6 24.1 1.0
CD1 C:TYR41 4.6 69.2 1.0
N C:TYR228 4.7 34.9 1.0
CG C:TYR228 4.8 34.8 1.0
O C:HOH617 4.8 26.2 1.0
CA C:THR227 4.9 35.2 1.0

Fluorine binding site 8 out of 12 in 7fqk

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Fluorine binding site 8 out of 12 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:40.5
occ:1.00
 F17 C:WS9501 0.0 40.5 1.0
C15 C:WS9501 1.4 45.9 1.0
O14 C:WS9501 2.1 36.0 1.0
F18 C:WS9501 2.2 42.6 1.0
F16 C:WS9501 2.3 43.5 1.0
O C:HOH625 3.1 24.1 1.0
CG C:TYR41 3.3 66.5 1.0
CB C:TYR41 3.5 60.5 1.0
C11 C:WS9501 3.5 34.4 1.0
O C:HOH644 3.6 25.2 1.0
CD1 C:TYR41 3.6 69.2 1.0
CD2 C:TYR41 3.7 70.4 1.0
CE1 C:TYR41 4.2 70.7 1.0
CA C:TYR41 4.3 55.6 1.0
CE2 C:TYR41 4.3 71.8 1.0
C12 C:WS9501 4.4 32.6 1.0
C10 C:WS9501 4.4 32.4 1.0
CZ C:TYR41 4.6 72.7 1.0
O C:TYR41 4.7 52.2 1.0
O C:HOH719 4.8 51.0 1.0
C C:TYR41 4.9 51.3 1.0

Fluorine binding site 9 out of 12 in 7fqk

Go back to Fluorine Binding Sites List in 7fqk
Fluorine binding site 9 out of 12 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F501

b:42.6
occ:1.00
 F18 C:WS9501 0.0 42.6 1.0
C15 C:WS9501 1.4 45.9 1.0
F17 C:WS9501 2.2 40.5 1.0
F16 C:WS9501 2.3 43.5 1.0
O14 C:WS9501 2.3 36.0 1.0
C11 C:WS9501 2.9 34.4 1.0
O C:HOH625 3.1 24.1 1.0
O C:HOH644 3.1 25.2 1.0
C12 C:WS9501 3.2 32.6 1.0
O C:HOH719 3.7 51.0 1.0
C10 C:WS9501 4.0 32.4 1.0
CE2 C:TYR228 4.0 35.0 1.0
C13 C:WS9501 4.4 30.1 1.0
CD2 C:TYR228 4.5 34.8 1.0
CE1 C:TYR221 5.0 49.9 1.0
C9 C:WS9501 5.0 33.1 1.0

Fluorine binding site 10 out of 12 in 7fqk

Go back to Fluorine Binding Sites List in 7fqk
Fluorine binding site 10 out of 12 in the Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of Human Legumain in Complex with (2S)-N-[(3S)-5- Amino-1-(1,3-Oxazol-2-Yl)-5-Oxopent-1-Yn-3-Yl]-1-[1-[4- (Trifluoromethoxy)Phenyl]Cyclopropanecarbonyl]Pyrrolidine-2- Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F503

b:35.7
occ:1.00
 F16 D:WS9503 0.0 35.7 1.0
C15 D:WS9503 1.3 36.0 1.0
F18 D:WS9503 2.2 34.8 1.0
O14 D:WS9503 2.2 32.0 1.0
F17 D:WS9503 2.2 35.5 1.0
C11 D:WS9503 2.7 30.4 1.0
C10 D:WS9503 2.8 27.7 1.0
O D:HOH618 2.9 23.7 1.0
O D:HOH628 3.2 29.0 1.0
O D:TYR41 3.2 35.9 1.0
CB D:TYR41 3.6 37.0 1.0
NH1 D:ARG44 3.7 35.5 1.0
C D:TYR41 3.9 36.1 1.0
C12 D:WS9503 3.9 29.9 1.0
CA D:TYR41 4.0 36.7 1.0
C9 D:WS9503 4.1 27.8 1.0
CG D:TYR41 4.3 37.7 1.0
CZ D:ARG44 4.7 35.5 1.0
O A:HOH647 4.7 31.1 1.0
NH2 D:ARG44 4.8 35.9 1.0
CD2 D:TYR228 4.9 34.1 1.0
O A:HOH671 4.9 39.4 1.0
CD2 D:TYR41 4.9 38.2 1.0
C13 D:WS9503 4.9 29.4 1.0
N D:ASN42 4.9 36.1 1.0
OD1 D:ASN42 5.0 36.3 1.0
CD1 D:TYR41 5.0 38.1 1.0

Reference:

B.Bartels, B.Kuhn, J.Benz, M.G.Rudolph. Crystal Structure of A Human Legumain Complex To Be Published.
Page generated: Fri Aug 2 07:08:09 2024

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