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EFEB_ECOLI_35_423

Deferrochelatase/peroxidase EfeB [DyP-type peroxidase family. EfeB subfamily]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (EFEB_ECOLI):R: Heme binding (236:238)
R: Heme binding (334, 336)
229, 231, 233:235, 275, 277, 294, 296, 329, 330, 333, 345, 347, 366, 368, 379, 382, 383, 386, 391, 395
229, 231, 233:238, 275, 277, 294, 296, 329, 330, 333, 334, 336, 345, 347, 366, 368, 379, 382, 383, 386, 391, 395
Metals (Me):Fe

Full PDB list

2y4d, 2y4e, 2y4f, 3o72

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
N
2
2
9
L
2
3
1
F
2
3
3
K
2
3
4
D
2
3
5
G
2
3
6
T
2
3
7
A
2
3
8
I
2
7
5
F
2
7
7
F
2
9
4
R
2
9
6
H
3
2
9
I
3
3
0
A
3
3
3
N
3
3
4
R
3
3
6
M
3
4
5
R
3
4
7
L
3
6
6
F
3
6
8
F
3
7
9
V
3
8
2
Q
3
8
3
L
3
8
6
L
3
9
1
V
3
9
5
[1]2y4d.a pg413 . . . . . . . . . . . . . . . . - . . . . . . . . . .
[1]2y4e.a pp942 . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2y4f.a hem42 . . . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]3o72.a hem42 . . . . . . . . . . . . . . . . . * . . . . . . . . . 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 Me
N
2
2
9
L
2
3
1
F
2
3
3
K
2
3
4
D
2
3
5
G
2
3
6
T
2
3
7
A
2
3
8
I
2
7
5
F
2
7
7
F
2
9
4
R
2
9
6
H
3
2
9
I
3
3
0
A
3
3
3
N
3
3
4
R
3
3
6
M
3
4
5
R
3
4
7
L
3
6
6
F
3
6
8
F
3
7
9
V
3
8
2
Q
3
8
3
L
3
8
6
L
3
9
1
V
3
9
5
[1]2y4d.a . . . . . . . . . . . . . . . . - . . . . . . . . . .
[1]2y4e.a . . . . . . . . . . . . . . . * . . . . . . . . . . .
[1]2y4f.a . . . . . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]3o72.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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
2y4d.a:pg4
2y4e.a:pp9
2y4f.a:hem
3o72.a:hem
[1] 2y4d.a
0
1.0 1.3 1.0
[1] 2y4e.a 0
0.1
1.0 0.8
[1] 2y4f.a 0 0.3
0.1
0
[1] 3o72.a 0.1 0.3 0
0.1
[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
2y4d.a
2y4e.a
2y4f.a
3o72.a
[1] 2y4d.a
0
.07 .07 .07
[1] 2y4e.a .07
0
.04 .05
[1] 2y4f.a .07 .04
0
.01
[1] 3o72.a .07 .05 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.7 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
2y4d.a
2y4e.a
2y4f.a
3o72.a
[1] 2y4d.a
0
0.5 0.7 0.6
[1] 2y4e.a 0.5
0
0.5 0.4
[1] 2y4f.a 0.7 0.5
0
0.2
[1] 3o72.a 0.6 0.4 0.2
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

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
2y4d.a
2y4e.a
2y4f.a
3o72.a
[1] 2y4d.a
0
0.7 0.9 0.8
[1] 2y4e.a 0.7
0
0.6 0.7
[1] 2y4f.a 0.9 0.6
0
0.6
[1] 3o72.a 0.8 0.7 0.6
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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