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CYB2_YEAST_181_591

Cytochrome b2, mitochondrial

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CYB2_YEAST):D: FMN hydroxy acid dehydrogenase (219, 223, 224, 275:279, 308, 310, 311, 332, 334, 360, 366, 369, 376, 405, 406, 429, 451, 453, 454, 456, 457, 489:491, 493, 511:513, 516)107, 109, 116, 119, 123:125, 129, 130, 138, 141, 142, 145:147, 150, 151, 154, 155, 177, 219, 223, 224, 275:279, 308, 310, 311, 332, 334, 360, 366, 369, 376, 405, 406, 429, 451, 453, 454, 456, 457, 489:491, 493, 511:513, 516
Metals (Me):Fe

Full PDB list

1fcb, 1kbi, 1kbj, 1lco, 1ldc, 1ltd, 1qcw, 1sze, 1szf, 1szg, 2oz0

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
V
1
0
7
I
1
0
9
L
1
1
6
F
1
1
9
H
1
2
3
P
1
2
4
G
1
2
5
V
1
2
9
I
1
3
0
V
1
3
8
I
1
4
1
F
1
4
2
L
1
4
5
H
1
4
6
A
1
4
7
V
1
5
0
I
1
5
1
Y
1
5
4
I
1
5
5
Y
1
7
7
Q
2
1
9
Y
2
2
3
Y
2
2
4
S
2
7
5
A
2
7
6
T
2
7
7
A
2
7
8
L
2
7
9
S
3
0
8
L
3
1
0
Q
3
3
2
Y
3
3
4
T
3
6
0
L
3
6
6
R
3
6
9
K
3
7
6
F
4
0
5
I
4
0
6
K
4
2
9
S
4
5
1
H
4
5
3
G
4
5
4
R
4
5
6
D
4
8
9
G
4
9
0
G
4
9
1
R
4
9
3
L
5
1
1
G
5
1
2
R
5
1
3
L
5
1
6
[1]1fcb.b fmn,pyr37 - - - - - - - - - - - - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kbi.a fmn,hem,res74 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]1kbj.a fmn31 - - - - - - - - - - - - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1lco.a fmn,hem,ppy,res86 . . . . . . . . . . . . . . . . . . . . . F . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]1lco.b fmn,ppy43 - - - - - - - - - - - - - - - - - - - - . F . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ldc.a fmn,hem,pyr,res80 . . . . . . . . . . . . . . . . . . . . . F . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]1ldc.b fmn,pyr37 - - - - - - - - - - - - - - - - - - - - . F . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ltd.a hem,res,so3.fmn78 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]1ltd.b so3.fmn35 - - - - - - - - - - - - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1qcw.a fns35 - - - - - - - - - - - - - - - - - - - - . . . . . . . . . . . . . . K . . . . . . . . . . . . . . . .
[1]1sze.a 173,fmn42 - - - - - - - - - - - - - - - - - - - - . . . . . . . . . A . . . . . . . . . . . . . . . . . . . . .
[1]1szf.a fmn,pyr37 - - - - - - - - - - - - - - - - - - - - . . . . . . G . . A . . . . . . . . . . . . . . . . . . . . .
[1]1szg.a fns35 - - - - - - - - - - - - - - - - - - - - . . . . . . G . . A . . . . . . . . . . . . . . . . . . . . .
[1]2oz0.a fe,fmn,hem74 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Q . . . . . . . . . .
[1]2oz0.b fmn,pyr37 - - - - - - - - - - - - - - - - - - - - . . . . . . . . . . . . . . . . . . . . Q . . . . . . . . . .

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 Me
V
1
0
7
I
1
0
9
L
1
1
6
F
1
1
9
H
1
2
3
P
1
2
4
G
1
2
5
V
1
2
9
I
1
3
0
V
1
3
8
I
1
4
1
F
1
4
2
L
1
4
5
H
1
4
6
A
1
4
7
V
1
5
0
I
1
5
1
Y
1
5
4
I
1
5
5
Y
1
7
7
Q
2
1
9
Y
2
2
3
Y
2
2
4
S
2
7
5
A
2
7
6
T
2
7
7
A
2
7
8
L
2
7
9
S
3
0
8
L
3
1
0
A
3
1
1
Q
3
3
2
Y
3
3
4
T
3
6
0
L
3
6
6
R
3
6
9
K
3
7
6
F
4
0
5
I
4
0
6
K
4
2
9
S
4
5
1
H
4
5
3
G
4
5
4
R
4
5
6
Q
4
5
7
D
4
8
9
G
4
9
0
G
4
9
1
R
4
9
3
L
5
1
1
G
5
1
2
R
5
1
3
L
5
1
6
[1]1fcb.b - - - - - - - - - - - - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kbi.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]1kbj.a - - - - - - - - - - - - - - - - - - - - . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . .
[1]1lco.a . . . . . . . . . . . . . . . . . . . . . F . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]1lco.b - - - - - - - - - - - - - - - - - - - - . F . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ldc.a . . . . . . . . . . . . . . . . . . . . . F . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]1ldc.b - - - - - - - - - - - - - - - - - - - - . F . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1ltd.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]1ltd.b - - - - - - - - - - - - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1qcw.a - - - - - - - - - - - - - - - - - - - - . . . . . . . . . * . . . . . K . . . . . . . . . . . . . . . . .
[1]1sze.a - - - - - - - - - - - - - - - - - - - - . . . . . . . . . A . . . . . . . . . . . . . . . . . . . . . . .
[1]1szf.a - - - - - - - - - - - - - - - - - - - - . . . . . . G . . A . . . . . . . . . . . . . . . . . . . . . . .
[1]1szg.a - - - - - - - - - - - - - - - - - - - - . . . . . . G . . A . . . . . . . . . . . . . . . . . . . . . . .
[1]2oz0.a . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Q . . . . . . * . . . .
[1]2oz0.b - - - - - - - - - - - - - - - - - - - - . . . . . . . . . . . . . . . . . . . . . Q . . . . . . . . . . .

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
1fcb.b:fmn,pyr
1kbi.a:fmn,hem,res
1kbj.a:fmn
1lco.a:fmn,hem,ppy,res
1lco.b:fmn,ppy
1ldc.a:fmn,hem,pyr,res
1ldc.b:fmn,pyr
1ltd.a:hem,res,so3.fmn
1ltd.b:so3.fmn
1qcw.a:fns
1sze.a:173,fmn
1szf.a:fmn,pyr
1szg.a:fns
2oz0.a:fe,fmn,hem
2oz0.b:fmn,pyr
[1] 1fcb.b
0.3
0.5 0.1 0.1 0.4 0.8 0.2 0.2 0.1 0.2 0.5 0.2 0.2 0.4 0.5
[1] 1kbi.a 0.5
0.3
0.1 1.0 0.2 1.1 0.3 1.0 0.3 0.1 0.5 0.2 0.1 0.5 0.5
[1] 1kbj.a 0.4 0.5
0
0.2 0.5 0.9 0.4 0.4 0.3 0.1 0.9 0.5 0.3 0.5 0.5
[1] 1lco.a 0.2 1.7 0
0.3
0.4 0.5 0.2 0.6 0.2 0.1 0.4 0.2 0.1 1.6 0.4
[1] 1lco.b 0.7 0.7 0.3 0.7
0.1
1.1 0.2 0.4 0.2 0.4 0.7 0.4 0.4 0.6 0.8
[1] 1ldc.a 0.3 1.3 0 0.3 0.4
0.3
0.3 0.4 0.3 0.1 0.6 0.2 0.1 1.1 0.5
[1] 1ldc.b 1.0 0.7 0.5 1.2 0.4 1.5
0.1
0.5 0.2 0.6 0.8 0.6 0.5 0.7 1.1
[1] 1ltd.a 0.4 2.2 0.1 1.0 0.4 1.2 0.3
0.3
0.1 0 0.6 0.5 0.1 1.3 0.7
[1] 1ltd.b 0.5 1.1 0.4 0.7 0.8 1.6 0.1 0.5
0.1
0.3 0.9 0.5 0.5 1.0 0.7
[1] 1qcw.a 0.5 1.0 0.2 0.5 0.8 1.5 0.6 0.4 0.5
0.1
1.5 0.9 0.4 1.0 0.7
[1] 1sze.a 0.6 0.5 0.3 0.5 0.4 1.0 0.5 0.3 0.4 0.4
0.5
0.4 0.3 0.5 0.7
[1] 1szf.a 0.5 0.1 0.1 0.4 0.2 0.5 0.4 0.2 0.3 0 0.2
0.1
0.1 0.1 0.7
[1] 1szg.a 0.8 0.9 0.3 0.5 0.9 1.0 0.7 0.6 0.4 0.3 0.5 0.4
0.3
0.9 1.2
[1] 2oz0.a 1.2 1.5 1.0 1.9 0.8 2.2 0.9 1.6 0.4 0.7 1.2 1.1 0.8
2.0
1.6
[1] 2oz0.b 0.7 1.0 0.5 0.8 0.9 1.6 0.7 0.5 0.7 0.6 1.0 0.9 0.4 1.0
0.8
[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
1fcb.b
1kbi.a
1kbj.a
1lco.a
1lco.b
1ldc.a
1ldc.b
1ltd.a
1ltd.b
1qcw.a
1sze.a
1szf.a
1szg.a
2oz0.a
2oz0.b
[1] 1fcb.b
0
.04 .02 .05 .03 .05 .05 .06 .03 .04 .02 .03 .04 .08 .03
[1] 1kbi.a .04
0
.05 .06 .05 .06 .06 .06 .07 .07 .05 .04 .06 .07 .05
[1] 1kbj.a .02 .05
0
.06 .04 .06 .05 .06 .04 .03 .03 .03 .04 .08 .04
[1] 1lco.a .05 .06 .06
0
.06 .03 .07 .04 .07 .06 .06 .06 .08 .08 .06
[1] 1lco.b .03 .05 .04 .06
0
.06 .03 .07 .02 .05 .03 .05 .04 .07 .03
[1] 1ldc.a .05 .06 .06 .03 .06
0
.07 .05 .07 .06 .06 .05 .08 .08 .06
[1] 1ldc.b .05 .06 .05 .07 .03 .07
0
.08 .03 .06 .05 .05 .06 .08 .04
[1] 1ltd.a .06 .06 .06 .04 .07 .05 .08
0
.07 .06 .07 .07 .08 .07 .06
[1] 1ltd.b .03 .07 .04 .07 .02 .07 .03 .07
0
.04 .05 .06 .04 .08 .03
[1] 1qcw.a .04 .07 .03 .06 .05 .06 .06 .06 .04
0
.04 .05 .04 .08 .04
[1] 1sze.a .02 .05 .03 .06 .03 .06 .05 .07 .05 .04
0
.01 .02 .07 .05
[1] 1szf.a .03 .04 .03 .06 .05 .05 .05 .07 .06 .05 .01
0
.02 .08 .04
[1] 1szg.a .04 .06 .04 .08 .04 .08 .06 .08 .04 .04 .02 .02
0
.07 .04
[1] 2oz0.a .08 .07 .08 .08 .07 .08 .08 .07 .08 .08 .07 .08 .07
0
.08
[1] 2oz0.b .03 .05 .04 .06 .03 .06 .04 .06 .03 .04 .05 .04 .04 .08
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.9 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
1fcb.b
1kbi.a
1kbj.a
1lco.a
1lco.b
1ldc.a
1ldc.b
1ltd.a
1ltd.b
1qcw.a
1sze.a
1szf.a
1szg.a
2oz0.a
2oz0.b
[1] 1fcb.b
0
0.3 0.3 0.4 0.4 0.5 0.6 0.4 0.4 0.5 0.4 0.4 0.4 0.5 0.6
[1] 1kbi.a 0.3
0
0.4 0.7 0.5 0.7 0.7 0.6 0.5 0.5 0.4 0.4 0.4 0.8 0.7
[1] 1kbj.a 0.3 0.4
0
0.3 0.4 0.4 0.6 0.3 0.4 0.4 0.4 0.4 0.3 0.5 0.6
[1] 1lco.a 0.4 0.7 0.3
0
0.5 0.4 0.6 0.5 0.4 0.5 0.4 0.4 0.3 0.7 0.6
[1] 1lco.b 0.4 0.5 0.4 0.5
0
0.5 0.4 0.5 0.4 0.5 0.5 0.5 0.5 0.6 0.5
[1] 1ldc.a 0.5 0.7 0.4 0.4 0.5
0
0.7 0.5 0.5 0.6 0.4 0.4 0.4 0.8 0.8
[1] 1ldc.b 0.6 0.7 0.6 0.6 0.4 0.7
0
0.6 0.4 0.6 0.6 0.7 0.6 0.7 0.5
[1] 1ltd.a 0.4 0.6 0.3 0.5 0.5 0.5 0.6
0
0.5 0.5 0.4 0.4 0.3 0.6 0.7
[1] 1ltd.b 0.4 0.5 0.4 0.4 0.4 0.5 0.4 0.5
0
0.5 0.5 0.5 0.4 0.6 0.6
[1] 1qcw.a 0.5 0.5 0.4 0.5 0.5 0.6 0.6 0.5 0.5
0
0.5 0.5 0.4 0.5 0.7
[1] 1sze.a 0.4 0.4 0.4 0.4 0.5 0.4 0.6 0.4 0.5 0.5
0
0.4 0.3 0.4 0.7
[1] 1szf.a 0.4 0.4 0.4 0.4 0.5 0.4 0.7 0.4 0.5 0.5 0.4
0
0.2 0.4 0.8
[1] 1szg.a 0.4 0.4 0.3 0.3 0.5 0.4 0.6 0.3 0.4 0.4 0.3 0.2
0
0.4 0.7
[1] 2oz0.a 0.5 0.8 0.5 0.7 0.6 0.8 0.7 0.6 0.6 0.5 0.4 0.4 0.4
0
0.7
[1] 2oz0.b 0.6 0.7 0.6 0.6 0.5 0.8 0.5 0.7 0.6 0.7 0.7 0.8 0.7 0.7
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
1fcb.b
1kbi.a
1kbj.a
1lco.a
1lco.b
1ldc.a
1ldc.b
1ltd.a
1ltd.b
1qcw.a
1sze.a
1szf.a
1szg.a
2oz0.a
2oz0.b
[1] 1fcb.b
0
0.7 0.8 0.9 0.9 0.9 1.1 0.9 0.9 1.0 0.8 0.7 0.9 0.8 0.9
[1] 1kbi.a 0.7
0
0.8 1.1 1.1 1.0 1.3 1.0 1.1 1.0 0.8 0.8 1.0 1.1 1.0
[1] 1kbj.a 0.8 0.8
0
1.0 1.0 1.0 1.2 0.9 0.9 1.1 0.7 0.7 0.9 0.8 1.0
[1] 1lco.a 0.9 1.1 1.0
0
1.0 0.6 1.0 0.7 0.9 1.1 0.9 0.9 0.9 1.2 1.1
[1] 1lco.b 0.9 1.1 1.0 1.0
0
0.9 0.9 0.9 0.6 0.9 1.0 1.0 0.9 1.1 1.1
[1] 1ldc.a 0.9 1.0 1.0 0.6 0.9
0
1.2 0.7 0.9 1.1 0.9 0.9 0.9 1.2 1.2
[1] 1ldc.b 1.1 1.3 1.2 1.0 0.9 1.2
0
1.1 0.8 1.1 1.2 1.2 1.1 1.1 1.0
[1] 1ltd.a 0.9 1.0 0.9 0.7 0.9 0.7 1.1
0
0.8 0.9 0.9 0.9 0.7 1.1 1.2
[1] 1ltd.b 0.9 1.1 0.9 0.9 0.6 0.9 0.8 0.8
0
1.0 0.9 1.0 0.8 1.0 1.1
[1] 1qcw.a 1.0 1.0 1.1 1.1 0.9 1.1 1.1 0.9 1.0
0
1.2 1.1 0.9 1.2 1.3
[1] 1sze.a 0.8 0.8 0.7 0.9 1.0 0.9 1.2 0.9 0.9 1.2
0
0.5 0.9 0.7 1.0
[1] 1szf.a 0.7 0.8 0.7 0.9 1.0 0.9 1.2 0.9 1.0 1.1 0.5
0
0.8 0.8 1.1
[1] 1szg.a 0.9 1.0 0.9 0.9 0.9 0.9 1.1 0.7 0.8 0.9 0.9 0.8
0
0.9 1.2
[1] 2oz0.a 0.8 1.1 0.8 1.2 1.1 1.2 1.1 1.1 1.0 1.2 0.7 0.8 0.9
0
1.1
[1] 2oz0.b 0.9 1.0 1.0 1.1 1.1 1.2 1.0 1.2 1.1 1.3 1.0 1.1 1.2 1.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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