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CPXM_BACME_1_410

Cytochrome P450(MEG) [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (CPXM_BACME):71, 73, 87:90, 173, 239, 240, 242, 243, 247, 39671, 73, 87:90, 173, 239, 240, 242, 243, 247, 396
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

4yt3, 5iki

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
I
7
1
V
7
3
I
8
8
T
8
9
E
9
0
F
1
7
3
I
2
4
0
A
2
4
3
T
2
4
7
[1]4yt3.a none - - . . . . . . . hem Fe
[1]5iki.b a9h22 . . . . . . . . . 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

[download in TSV format]
   
PDB.ch
A1 cF Me
I
7
1
V
7
3
Q
8
7
I
8
8
T
8
9
E
9
0
F
1
7
3
L
2
3
9
I
2
4
0
G
2
4
2
A
2
4
3
T
2
4
7
T
3
9
6
[1]4yt3.a - - . . . . . . . . . . . hem Fe
[1]5iki.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
4yt3.a is apo
5iki.b:a9h
[1] 4yt3.a
-
0.8
[1] 5iki.b -
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
4yt3.a
5iki.b
[1] 4yt3.a
0
.06
[1] 5iki.b .06
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.3 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
4yt3.a
5iki.b
[1] 4yt3.a
0
2.1
[1] 5iki.b 2.1
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

zoom: [−] [+]; [view as image]; [download as text]

pocketpocket
≥10 Å
9 Å
8 Å
7 Å
6 Å
5 Å
4 Å
3 Å
2 Å
1 Å
0 Å
4yt3.a
5iki.b
[1] 4yt3.a
0
2.5
[1] 5iki.b 2.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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