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.

C562_ECOLX_23_128_phen

Soluble cytochrome b562 [Cytochrome b562 family]

Composition of the binding site

Protein chains monomer
A1 (C562_ECOLX):63:65, 75:77, 80, 81, 83:8563:65, 75:77, 80, 81, 83:85
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

1lm3, 1m6t, 256b, 2bc5, 2qla, 3c62, 3c63, 3de8, 3de9, 3foo, 3fop, 3l1m, 3nmi, 3nmj, 3nmk (redundant Pocketome entry); 5awi (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
Q
6
3
K
6
4
A
6
5
P
7
5
D
7
6
M
8
0
K
8
1
F
8
3
R
8
4
H
8
5
[1]3c62.a zn1 . . . . . . H . D . hem Fe
[1]3c63.b none . . . . . . H . D . hem Fe
[1]3foo.c ni,pxx19 . . . . . . C . A A hem Fe
[1]3nmi.c pxx,pxx36 . . . . . . C . A A hem Fe
[1]3nmi.d pxx18 . . . . . . C . A A hem Fe
[1]3nmk.b pxx,zn19 . . . . . . C . A A hem Fe
[2]1lm3.b none . . . . . . . I . . hem Fe
[2]3de8.a cu1 . . . . . . H . . . hem Fe
[3]256b.a none . . . . . . . . . . hem Fe
[3]3de9.a none . . . . . . H . . . hem
[4]2bc5.a none . . . . . . W . . . 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
Q
6
3
K
6
4
A
6
5
P
7
5
D
7
6
S
7
7
M
8
0
K
8
1
F
8
3
R
8
4
H
8
5
[1]3c62.a . . . . . . . H . D . hem Fe
[1]3c63.b . . . . . . . H . D . hem Fe
[1]3foo.c . . . . . . . C . A A hem Fe
[1]3nmi.c . . . . . . . C . A A hem Fe
[1]3nmi.d . . . . . . . C . A A hem Fe
[1]3nmk.b . . . . . . . C . A A hem Fe
[2]1lm3.b . . . . . . . * I * . hem Fe
[2]3de8.a . . . . . . . H . * . hem Fe
[3]256b.a . . . . . . . * . * . hem Fe
[3]3de9.a . . . . . . . H . * . hem
[4]2bc5.a . . . . . . . W . * . 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

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

pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
3c62.a:zn
3c63.b is apo
3foo.c:ni,pxx
3nmi.c:pxx
3nmi.d:pxx
3nmk.b:pxx,zn
1lm3.b is apo
3de8.a:cu
256b.a is apo
3de9.a is apo
2bc5.a is apo
[1] 3c62.a
0.1
- 0.6 0.7 2.4 0.6 - 0.2 - - -
[1] 3c63.b 0.4
-
0.6 1.0 3.0 0.7 - 0.4 - - -
[1] 3foo.c 0 -
0.4
0.6 0.6 0.4 - 0 - - -
[1] 3nmi.c 0 - 0.4
0.4
0.4 0.4 - 0 - - -
[1] 3nmi.d 0 - 0.4 0.3
0.4
0.1 - 0 - - -
[1] 3nmk.b 0 - 0.6 0.6 0.6
0.4
- 0 - - -
[2] 1lm3.b 0 - 0.3 2.5 1.3 0.2
-
0 - - -
[2] 3de8.a 0 - 0.5 2.1 1.3 0.5 -
0.2
- - -
[3] 256b.a 0 - 4.7 5.3 1.7 4.4 - 0
-
- -
[3] 3de9.a 0.4 - 3.9 5.0 3.3 3.8 - 0.5 -
-
-
[4] 2bc5.a 0 - 6.8 8.7 2.7 6.4 - 0 - -
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (4 clusters)

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
3c62.a
3c63.b
3foo.c
3nmi.c
3nmi.d
3nmk.b
1lm3.b
3de8.a
256b.a
3de9.a
2bc5.a
[1] 3c62.a
0
.07 .17 .18 .18 .17 .27 .26 .33 .42 .54
[1] 3c63.b .07
0
.22 .23 .22 .22 .32 .31 .36 .36 .48
[1] 3foo.c .17 .22
0
.02 .03 0 .23 .22 .41 .57 .69
[1] 3nmi.c .18 .23 .02
0
.01 .02 .25 .24 .43 .59 .71
[1] 3nmi.d .18 .22 .03 .01
0
.03 .24 .23 .42 .58 .70
[1] 3nmk.b .17 .22 0 .02 .03
0
.23 .22 .41 .57 .69
[2] 1lm3.b .27 .32 .23 .25 .24 .23
0
.08 .17 .34 .46
[2] 3de8.a .26 .31 .22 .24 .23 .22 .08
0
.25 .40 .53
[3] 256b.a .33 .36 .41 .43 .42 .41 .17 .25
0
.17 .30
[3] 3de9.a .42 .36 .57 .59 .58 .57 .34 .40 .17
0
.25
[4] 2bc5.a .54 .48 .69 .71 .70 .69 .46 .53 .30 .25
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

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
3c62.a
3c63.b
3foo.c
3nmi.c
3nmi.d
3nmk.b
1lm3.b
3de8.a
256b.a
3de9.a
2bc5.a
[1] 3c62.a
0
0.5 0.8 0.4 0.7 0.6 0.6 0.6 0.8 0.8 0.6
[1] 3c63.b 0.5
0
0.9 0.7 0.8 0.7 0.8 0.9 0.6 0.6 0.5
[1] 3foo.c 0.8 0.9
0
0.6 0.3 0.3 0.6 0.8 1.1 1.0 0.7
[1] 3nmi.c 0.4 0.7 0.6
0
0.5 0.4 0.5 0.6 0.7 0.8 0.5
[1] 3nmi.d 0.7 0.8 0.3 0.5
0
0.3 0.6 0.6 1.0 0.9 0.7
[1] 3nmk.b 0.6 0.7 0.3 0.4 0.3
0
0.5 0.7 0.9 0.9 0.6
[2] 1lm3.b 0.6 0.8 0.6 0.5 0.6 0.5
0
0.8 1.0 0.9 0.7
[2] 3de8.a 0.6 0.9 0.8 0.6 0.6 0.7 0.8
0
1.1 1.1 0.8
[3] 256b.a 0.8 0.6 1.1 0.7 1.0 0.9 1.0 1.1
0
0.4 0.5
[3] 3de9.a 0.8 0.6 1.0 0.8 0.9 0.9 0.9 1.1 0.4
0
0.4
[4] 2bc5.a 0.6 0.5 0.7 0.5 0.7 0.6 0.7 0.8 0.5 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.6 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
3c62.a
3c63.b
3foo.c
3nmi.c
3nmi.d
3nmk.b
1lm3.b
3de8.a
256b.a
3de9.a
2bc5.a
[1] 3c62.a
0
1.0 1.6 1.3 1.5 1.2 1.6 1.3 1.2 1.4 1.2
[1] 3c63.b 1.0
0
1.3 1.1 1.2 0.9 1.4 1.4 1.0 1.5 1.1
[1] 3foo.c 1.6 1.3
0
1.1 0.8 0.7 0.8 1.1 1.5 1.8 1.2
[1] 3nmi.c 1.3 1.1 1.1
0
0.8 0.7 1.1 1.1 1.3 1.5 0.9
[1] 3nmi.d 1.5 1.2 0.8 0.8
0
0.6 1.0 1.0 1.5 1.7 0.9
[1] 3nmk.b 1.2 0.9 0.7 0.7 0.6
0
0.9 0.9 1.2 1.4 0.9
[2] 1lm3.b 1.6 1.4 0.8 1.1 1.0 0.9
0
1.6 1.8 2.3 1.6
[2] 3de8.a 1.3 1.4 1.1 1.1 1.0 0.9 1.6
0
1.8 1.8 1.9
[3] 256b.a 1.2 1.0 1.5 1.3 1.5 1.2 1.8 1.8
0
1.2 0.9
[3] 3de9.a 1.4 1.5 1.8 1.5 1.7 1.4 2.3 1.8 1.2
0
1.5
[4] 2bc5.a 1.2 1.1 1.2 0.9 0.9 0.9 1.6 1.9 0.9 1.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

loading...