Iodine in PDB 6nyh: Structure of Human RIPK1 Kinase Domain in Complex with GNE684

Enzymatic activity of Structure of Human RIPK1 Kinase Domain in Complex with GNE684

All present enzymatic activity of Structure of Human RIPK1 Kinase Domain in Complex with GNE684:
2.7.11.1;

Protein crystallography data

The structure of Structure of Human RIPK1 Kinase Domain in Complex with GNE684, PDB code: 6nyh was solved by R.Fong, P.J.Lupardus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.52 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 46.980, 97.034, 125.238, 90.00, 90.00, 90.00
R / Rfree (%) 20.3 / 24.6

Iodine Binding Sites:

The binding sites of Iodine atom in the Structure of Human RIPK1 Kinase Domain in Complex with GNE684 (pdb code 6nyh). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Structure of Human RIPK1 Kinase Domain in Complex with GNE684, PDB code: 6nyh:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in 6nyh

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Iodine binding site 1 out of 6 in the Structure of Human RIPK1 Kinase Domain in Complex with GNE684


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Structure of Human RIPK1 Kinase Domain in Complex with GNE684 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I302

b:73.4
occ:1.00
 CG A:GLU282 3.9 40.4 1.0
NE A:ARG286 4.0 33.5 1.0
CB B:SER73 4.0 38.7 1.0
CA B:SER73 4.0 35.0 1.0
CD A:ARG286 4.1 36.4 1.0
CA A:GLU283 4.1 43.5 1.0
OE2 A:GLU282 4.2 41.9 1.0
NZ B:LYS77 4.2 53.3 1.0
CG A:GLU283 4.2 51.9 1.0
CD A:GLU282 4.2 43.3 1.0
O A:GLU282 4.3 33.9 1.0
N A:GLU283 4.3 36.3 1.0
C A:GLU282 4.4 34.9 1.0
N B:SER73 4.6 33.2 1.0
CB A:ARG286 4.6 33.2 1.0
CB A:GLU283 4.7 41.9 1.0
CB A:GLU282 4.8 35.2 1.0
CG A:ARG286 5.0 35.9 1.0

Iodine binding site 2 out of 6 in 6nyh

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Iodine binding site 2 out of 6 in the Structure of Human RIPK1 Kinase Domain in Complex with GNE684


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Structure of Human RIPK1 Kinase Domain in Complex with GNE684 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I303

b:50.7
occ:1.00
 O A:HOH458 3.1 35.4 1.0
CB A:LYS284 3.9 39.5 1.0
CA A:PHE285 3.9 32.9 1.0
C A:LYS284 4.1 38.8 1.0
N A:PHE285 4.1 34.1 1.0
O A:LYS284 4.2 38.8 1.0
CB A:PHE285 4.3 34.5 1.0
CD1 A:PHE285 4.3 32.0 1.0
CD2 A:LEU263 4.4 33.3 1.0
CB A:PHE288 4.4 43.6 1.0
O A:GLU259 4.4 33.5 1.0
CB A:GLU259 4.4 43.6 1.0
CG A:PHE288 4.6 45.0 1.0
CA A:LYS284 4.6 38.9 1.0
CD2 A:PHE288 4.7 36.7 1.0
CB A:LEU263 4.8 31.4 1.0
CG A:PHE285 4.8 34.7 1.0
CD A:LYS284 4.8 48.3 1.0
C A:GLU259 4.9 33.9 1.0
CG A:LYS284 5.0 45.5 1.0

Iodine binding site 3 out of 6 in 6nyh

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Iodine binding site 3 out of 6 in the Structure of Human RIPK1 Kinase Domain in Complex with GNE684


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Structure of Human RIPK1 Kinase Domain in Complex with GNE684 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I304

b:1.0
occ:1.00
 N A:GLU234 4.0 38.3 1.0
CA A:GLU234 4.0 41.5 1.0
C A:ALA233 4.1 39.1 1.0
O A:HOH453 4.1 36.2 1.0
CD2 A:LEU237 4.1 34.0 1.0
O A:ALA233 4.2 36.6 1.0
CB A:ALA231 4.5 32.9 1.0
CB A:LEU237 4.6 38.2 1.0
CB A:GLU234 4.6 42.6 1.0
O A:ILE232 4.8 37.7 1.0
CA A:ALA233 4.8 39.8 1.0
N A:ALA233 4.8 35.7 1.0
C A:ILE232 4.8 37.8 1.0
OH A:TYR191 4.8 40.4 1.0
CE1 A:TYR191 4.9 35.2 1.0
O A:ALA231 4.9 33.0 1.0

Iodine binding site 4 out of 6 in 6nyh

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Iodine binding site 4 out of 6 in the Structure of Human RIPK1 Kinase Domain in Complex with GNE684


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Structure of Human RIPK1 Kinase Domain in Complex with GNE684 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I302

b:56.7
occ:1.00
 N B:ILE232 3.6 57.4 1.0
CG1 B:ILE232 3.7 54.7 1.0
CD1 B:ILE232 3.7 52.4 1.0
CA B:ALA231 3.9 55.4 1.0
CB B:ALA231 4.0 54.1 1.0
CA B:LEU237 4.0 38.6 1.0
N B:LEU237 4.2 41.2 1.0
C B:ALA231 4.3 58.0 1.0
CD1 B:LEU237 4.3 39.5 1.0
CB B:LEU237 4.4 41.3 1.0
CB B:ILE232 4.4 57.9 1.0
C B:GLN236 4.5 37.8 1.0
O B:GLN236 4.5 40.4 1.0
CA B:ILE232 4.6 59.6 1.0
CB B:ALA240 4.7 33.0 1.0
CB B:GLN236 4.9 42.8 1.0
O B:HOH484 5.0 36.0 1.0
CG B:LEU237 5.0 39.0 1.0

Iodine binding site 5 out of 6 in 6nyh

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Iodine binding site 5 out of 6 in the Structure of Human RIPK1 Kinase Domain in Complex with GNE684


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Structure of Human RIPK1 Kinase Domain in Complex with GNE684 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I303

b:54.6
occ:1.00
 O B:HOH461 3.1 36.5 1.0
CA B:PHE285 4.0 31.0 1.0
O B:LYS284 4.0 38.8 1.0
CD B:LYS284 4.1 55.6 1.0
C B:LYS284 4.1 39.1 1.0
CD1 B:PHE285 4.1 29.5 1.0
CB B:GLU259 4.1 31.1 1.0
N B:PHE285 4.2 34.6 1.0
CB B:LYS284 4.2 45.8 1.0
CG B:LYS284 4.3 54.3 1.0
O B:GLU259 4.3 25.7 1.0
CB B:PHE285 4.3 32.5 1.0
CB B:PHE288 4.5 32.0 1.0
CD2 B:PHE288 4.7 34.4 1.0
CD2 B:LEU263 4.7 28.2 1.0
CG B:GLU259 4.7 34.0 1.0
CG B:PHE285 4.7 30.2 1.0
CG B:PHE288 4.7 30.3 1.0
C B:GLU259 4.8 30.0 1.0
CA B:LYS284 4.8 41.7 1.0
CB B:LEU263 4.9 28.0 1.0
CA B:GLU259 5.0 33.4 1.0

Iodine binding site 6 out of 6 in 6nyh

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Iodine binding site 6 out of 6 in the Structure of Human RIPK1 Kinase Domain in Complex with GNE684


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Structure of Human RIPK1 Kinase Domain in Complex with GNE684 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I304

b:72.6
occ:1.00
 O A:HOH489 3.2 45.4 1.0
NE B:ARG286 3.9 34.7 1.0
CA A:SER73 3.9 34.6 1.0
CG B:GLU282 4.0 35.2 1.0
CD B:ARG286 4.0 36.2 1.0
CB A:SER73 4.0 35.6 1.0
CG B:GLU283 4.1 58.5 1.0
CA B:GLU283 4.2 50.2 1.0
CD B:GLU282 4.2 41.2 1.0
OE2 B:GLU282 4.2 38.6 1.0
O B:GLU282 4.3 41.1 1.0
N A:SER73 4.4 30.2 1.0
NZ A:LYS77 4.5 55.3 1.0
N B:GLU283 4.5 39.8 1.0
C B:GLU282 4.5 37.0 1.0
CB B:ARG286 4.6 35.1 1.0
CB B:GLU283 4.7 50.1 1.0
CB B:GLU282 4.8 32.3 1.0
C A:HIS72 4.8 29.6 1.0
OE1 B:GLU282 4.9 42.2 1.0
CG B:ARG286 4.9 40.6 1.0
O A:HIS72 4.9 30.4 1.0

Reference:

S.Patel, J.D.Webster, E.Varfolomeev, Y.C.Kwon, J.H.Cheng, J.Zhang, D.L.Dugger, K.E.Wickliffe, A.Maltzman, S.Sujatha-Bhaskar, P.Bir Kohli, S.Ramaswamy, G.Deshmukh, B.M.Liederer, R.Fong, G.Hamilton, P.Lupardus, P.Caplazi, W.P.Lee, M.Van Lookeren Campagne, A.Johnson, B.S.Mckenzie, M.R.Junttila, K.Newton, D.Vucic. RIP1 Inhibition Blocks Inflammatory Diseases But Not Tumor Growth or Metastases. Cell Death Differ. 2019.
ISSN: ISSN 1350-9047
PubMed: 31101885
DOI: 10.1038/S41418-019-0347-0
Page generated: Sun Dec 13 19:46:55 2020

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