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ARNA_ECOLI_1_306

Bifunctional polymyxin resistance protein ArnA

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ARNA_ECOLI):R: Formyltransferase ArnAFT (9, 38, 42, 83:85, 104, 113:116, 118, 200:203, 224, 228, 229)9, 38, 42, 83:85, 104, 113:116, 118, 200:203, 224, 228, 229

Full PDB list

1yrw, 1z7e, 2bln, 4wkg, 5j63 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
E
3
8
Y
4
2
Y
8
3
Y
8
4
R
8
5
H
1
0
4
R
1
1
4
A
1
1
5
P
1
1
6
N
1
1
8
R
2
0
0
R
2
0
1
T
2
0
2
P
2
0
3
V
2
2
4
W
2
2
8
P
2
2
9
[1]1yrw.a none - . . . . . . . . . . . . . . . .
[1]2bln.a u5p21 - . . . . . . . . . . . . . . . .
[1]5j63.c g3n34 . . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Site contact map

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PDB.ch
A1
H
9
E
3
8
Y
4
2
Y
8
3
Y
8
4
R
8
5
H
1
0
4
G
1
1
3
R
1
1
4
A
1
1
5
P
1
1
6
N
1
1
8
R
2
0
0
R
2
0
1
T
2
0
2
P
2
0
3
V
2
2
4
W
2
2
8
P
2
2
9
[1]1yrw.a . - . . . . . . . . . . . . . . . . .
[1]2bln.a . - . . . . . . . . . . . . . . . . .
[1]5j63.c . . . . . . . . . . . . . . . . . . .

Legend

B backbone contact  S side chain contact  F BB + SCh
.
 no contact C covalent bond
X X X X X  clash
X mutation to X * complex cases - deletion
M contact with cofactors/metals (if any)

Pocket-ligand steric compatibility

Ligands (x) vs pockets (y) colored by number of steric clashes

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1yrw.a is apo
2bln.a:u5p
5j63.c:g3n
[1] 1yrw.a
-
0.7 0.2
[1] 2bln.a -
0.1
0.4
[1] 5j63.c - 1.2
0.1
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

Pockets (x) vs pockets (y) colored by ligand clash profile difference

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pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
1yrw.a
2bln.a
5j63.c
[1] 1yrw.a
0
.02 .07
[1] 2bln.a .02
0
.07
[1] 5j63.c .07 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.4 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1yrw.a
2bln.a
5j63.c
[1] 1yrw.a
0
0.8 1.2
[1] 2bln.a 0.8
0
0.8
[1] 5j63.c 1.2 0.8
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.7 Å)

Pockets (x) vs pockets (y) colored by RMSD of all site residue atoms

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pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
1yrw.a
2bln.a
5j63.c
[1] 1yrw.a
0
1.4 1.4
[1] 2bln.a 1.4
0
1.5
[1] 5j63.c 1.4 1.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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