If you see this message after the page is completely loaded, then JavaScript is not supported or disabled in your browser. Please consider enabling JavaScript for this site.

CYCP_ALCXX_1_127

Cytochrome c'

Composition of the binding site

Protein chains monomer
A1 (CYCP_ALCXX):20, 23, 113, 116, 117, 12020, 23, 113, 116, 117, 120
Cofactors (cF):hec
Metals (Me):Fe

Full PDB list

1cgn, 1cgo, 1e83, 1e84, 1e85, 1e86, 2xl6, 2xl8, 2xld, 2xle, 2xlh, 2xlm, 2xlo, 2xlv, 2xlw, 2xm0, 2xm4, 2ykz, 2yl0, 2yl1, 2yl3, 2yl7, 2yld, 2ylg, 2yli, 3zqv, 3zqy, 3ztm, 3ztz, 3zwi, 4cda, 4cdv, 4cdy, 4cip, 4cjg, 4cjo, 4d4n, 4d4x, 4wgy, 4wgz, 5agf, 5jli, 5jp7, 5jra, 5js5, 5jsl, 5jt4, 5jua, 5jve, 5nc0 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
A
2
0
F
2
3
G
1
1
3
C
1
1
6
H
1
2
0
[1]2xld.a none . . . . . hec Fe
[1]2ykz.a none . . . . . Fe
[1]2ylg.a asc12 . . . . . Fe
[1]5agf.a none . . . . . 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
A
2
0
F
2
3
G
1
1
3
C
1
1
6
K
1
1
7
H
1
2
0
[1]2xld.a . . . . . . hec Fe
[1]2ykz.a . . . . . . Fe
[1]2ylg.a . . . . . . Fe
[1]5agf.a . . . . . . 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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
2xld.a is apo
2ykz.a is apo
2ylg.a:asc
5agf.a is apo
[1] 2xld.a
-
- 0.1 -
[1] 2ykz.a -
-
0 -
[1] 2ylg.a - -
0
-
[1] 5agf.a - - 0
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (1 cluster)

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

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

pocketpocket
≥1.
.9
.8
.7
.6
.5
.4
.3
.2
.1
.0
2xld.a
2ykz.a
2ylg.a
5agf.a
[1] 2xld.a
0
.02 .02 .02
[1] 2ykz.a .02
0
0 0
[1] 2ylg.a .02 0
0
0
[1] 5agf.a .02 0 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 Å)

Pockets (x) vs pockets (y) colored by RMSD of site residue backbone 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
2xld.a
2ykz.a
2ylg.a
5agf.a
[1] 2xld.a
0
0.5 0.3 0.3
[1] 2ykz.a 0.5
0
0.3 0.7
[1] 2ylg.a 0.3 0.3
0
0.4
[1] 5agf.a 0.3 0.7 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
2xld.a
2ykz.a
2ylg.a
5agf.a
[1] 2xld.a
0
0.5 0.4 1.3
[1] 2ykz.a 0.5
0
0.5 1.6
[1] 2ylg.a 0.4 0.5
0
1.6
[1] 5agf.a 1.3 1.6 1.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

L C X E | Background Color: | Anaglyph Stereo:

loading...