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CYPX_BACSU_1_405

Pulcherriminic acid synthase [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CYPX_BACSU):64, 162, 165, 166, 232, 233, 236, 237, 280, 391, 39264, 162, 165, 166, 232, 233, 236, 237, 280, 391, 392
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

3nc3, 3nc5, 3nc6, 3nc7 (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 cF Me
L
6
4
A
1
6
2
I
1
6
5
T
1
6
6
L
2
3
2
E
2
3
6
V
2
8
0
Y
3
9
1
T
3
9
2
[1]3nc5.a none . . . . . . . . . hem Fe
[1]3nc6.a piw11 . . . . . . . . . hem Fe
[1]3nc7.b piy11 . . . . . . . . . hem Fe

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 cF Me
L
6
4
A
1
6
2
I
1
6
5
T
1
6
6
L
2
3
2
A
2
3
3
E
2
3
6
P
2
3
7
V
2
8
0
Y
3
9
1
T
3
9
2
[1]3nc5.a . . . . . . . . . . . hem Fe
[1]3nc6.a . . . . . . . . . . . hem Fe
[1]3nc7.b . . . . . . . . . . . hem Fe

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
3nc5.a is apo
3nc6.a:piw
3nc7.b:piy
[1] 3nc5.a
-
0.4 0.5
[1] 3nc6.a -
0
0.1
[1] 3nc7.b - 0
0
[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
3nc5.a
3nc6.a
3nc7.b
[1] 3nc5.a
0
.04 .05
[1] 3nc6.a .04
0
.01
[1] 3nc7.b .05 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
3nc5.a
3nc6.a
3nc7.b
[1] 3nc5.a
0
2.3 2.3
[1] 3nc6.a 2.3
0
0.4
[1] 3nc7.b 2.3 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.4 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
3nc5.a
3nc6.a
3nc7.b
[1] 3nc5.a
0
2.7 3.0
[1] 3nc6.a 2.7
0
1.2
[1] 3nc7.b 3.0 1.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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