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COAD_MYCTU_2_157

Phosphopantetheine adenylyltransferase [Bacterial CoaD family]

Composition of the binding site

Protein chains monomer
A1 (COAD_MYCTU):7:10, 16, 17, 20, 36, 38, 41, 71:73, 87:90, 93, 94, 97, 98, 101, 104, 105, 118, 122, 125:1287:10, 16, 17, 20, 36, 38, 41, 71:73, 87:90, 93, 94, 97, 98, 101, 104, 105, 118, 122, 125:128

Full PDB list

1tfu, 3lcj, 3nba, 3nbk, 3pnb, 3rba, 3rff, 3rhs, 3uc5, 4e1a, 4r0n (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1
P
7
G
8
S
9
F
1
0
G
1
6
H
1
7
I
2
0
L
3
6
G
7
1
L
7
2
V
7
3
K
8
7
G
8
8
R
9
0
D
9
4
Y
9
7
E
9
8
M
1
0
1
M
1
0
4
N
1
0
5
T
1
1
8
Y
1
2
2
V
1
2
5
S
1
2
6
S
1
2
7
S
1
2
8
[1]3nba.a apc,mg32 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3nba.b apc31 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3nbk.a pns22 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3pnb.a coa48 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3rba.a cod44 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3uc5.a atp31 . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4e1a.a none . . . . . . . . . . . . . . . . . . . . . . . . . .

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
P
7
G
8
S
9
F
1
0
G
1
6
H
1
7
I
2
0
L
3
6
N
3
8
K
4
1
G
7
1
L
7
2
V
7
3
K
8
7
G
8
8
L
8
9
R
9
0
T
9
3
D
9
4
Y
9
7
E
9
8
M
1
0
1
M
1
0
4
N
1
0
5
T
1
1
8
Y
1
2
2
V
1
2
5
S
1
2
6
S
1
2
7
S
1
2
8
[1]3nba.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3nba.b . . . . . . . . . . . . . . . . . . . . . * . . . . . . . .
[1]3nbk.a . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]3pnb.a . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .
[1]3rba.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]3uc5.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]4e1a.a . . . . . . . . . . . . . . . . . . . . . . . . * . . . . .

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
3nba.a:apc,mg
3nba.b:apc
3nbk.a:pns
3pnb.a:coa
3rba.a:cod
3uc5.a:atp
4e1a.a is apo
[1] 3nba.a
0.1
0.1 0.5 1.0 0.6 0.2 -
[1] 3nba.b 0.2
0.1
0.9 1.4 1.4 0.3 -
[1] 3nbk.a 1.7 1.6
0
0.2 0.7 1.0 -
[1] 3pnb.a 1.1 1.6 0
0
0.8 1.0 -
[1] 3rba.a 0.3 0.5 0 0.1
0
0.1 -
[1] 3uc5.a 0.5 0.3 0.1 0.1 0.2
0.1
-
[1] 4e1a.a 1.4 1.8 0.1 0.2 1.0 1.1
-
[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
3nba.a
3nba.b
3nbk.a
3pnb.a
3rba.a
3uc5.a
4e1a.a
[1] 3nba.a
0
.04 .11 .09 .05 .06 .10
[1] 3nba.b .04
0
.12 .11 .07 .08 .12
[1] 3nbk.a .11 .12
0
.05 .07 .07 .06
[1] 3pnb.a .09 .11 .05
0
.06 .06 .01
[1] 3rba.a .05 .07 .07 .06
0
.02 .07
[1] 3uc5.a .06 .08 .07 .06 .02
0
.07
[1] 4e1a.a .10 .12 .06 .01 .07 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.9 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
3nba.a
3nba.b
3nbk.a
3pnb.a
3rba.a
3uc5.a
4e1a.a
[1] 3nba.a
0
0.7 1.3 1.3 0.8 1.0 1.4
[1] 3nba.b 0.7
0
1.5 1.5 0.4 0.8 1.2
[1] 3nbk.a 1.3 1.5
0
0.3 1.5 1.3 1.1
[1] 3pnb.a 1.3 1.5 0.3
0
1.5 1.3 1.1
[1] 3rba.a 0.8 0.4 1.5 1.5
0
0.7 1.2
[1] 3uc5.a 1.0 0.8 1.3 1.3 0.7
0
1.2
[1] 4e1a.a 1.4 1.2 1.1 1.1 1.2 1.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.1 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
3nba.a
3nba.b
3nbk.a
3pnb.a
3rba.a
3uc5.a
4e1a.a
[1] 3nba.a
0
1.6 1.8 1.9 1.9 1.9 2.5
[1] 3nba.b 1.6
0
2.5 2.5 1.0 1.3 2.1
[1] 3nbk.a 1.8 2.5
0
0.7 2.7 2.5 2.1
[1] 3pnb.a 1.9 2.5 0.7
0
2.6 2.5 1.9
[1] 3rba.a 1.9 1.0 2.7 2.6
0
1.2 1.9
[1] 3uc5.a 1.9 1.3 2.5 2.5 1.2
0
2.0
[1] 4e1a.a 2.5 2.1 2.1 1.9 1.9 2.0
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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