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BIOI_BACSU_2_395

Biotin biosynthesis cytochrome P450 [Cytochrome P450 family] / Acyl carrier protein (ACP_ECOLI) [Acyl carrier protein (ACP) family]

Composition of the binding site

Protein chains heterodimer [domain annotation]
A1 (BIOI_BACSU):R: Substrate binding (169, 171, 173)
R: Heme binding (285, 286)
37, 60:64, 77, 80, 82, 83, 165, 166, 168, 231, 234, 235, 239, 282, 284, 305, 307, 384
37, 60:64, 77, 80, 82, 83, 165, 166, 168, 169, 171, 173, 231, 234, 235, 239, 282, 284:286, 305, 307, 384
B1 (ACP_ECOLI):37
Cofactors (cF):hem/htg
Metals (Me):Fe

Full PDB list

3ejb, 3ejd, 3eje

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 B1 cF Me
Y
3
7
R
6
0
T
6
1
P
6
2
L
6
3
P
6
4
Q
7
7
M
8
0
L
8
2
L
1
6
5
I
1
6
6
I
1
6
9
F
1
7
1
R
1
7
3
L
2
3
1
I
2
3
4
A
2
3
5
T
2
3
9
T
2
8
2
M
2
8
4
T
2
8
5
A
2
8
6
Q
3
0
5
Y
3
0
7
F
3
8
4
S
3
7
[1]3ejb.b zmp36 . . . . . . . . . . . . . . . . . . . . . . . . . * hem,htg Fe
[1]3ejd.b zmq38 . . . . . . . . . . . . . . . . . . . . . . . . . * hem,htg Fe
[1]3eje.b zmo38 . . . . . . . . . . . . . . . . . . . . . . . . . * hem,htg 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 B1 cF Me
Y
3
7
R
6
0
T
6
1
P
6
2
L
6
3
P
6
4
Q
7
7
M
8
0
L
8
2
F
8
3
L
1
6
5
I
1
6
6
T
1
6
8
I
1
6
9
F
1
7
1
R
1
7
3
L
2
3
1
I
2
3
4
A
2
3
5
T
2
3
9
T
2
8
2
M
2
8
4
T
2
8
5
A
2
8
6
Q
3
0
5
Y
3
0
7
F
3
8
4
S
3
7
[1]3ejb.b . . . . . . . . . . . . . . . . . . . . . . . . . . . * hem,htg Fe
[1]3ejd.b . . . . . . . . . . . . . . . . . . . . . . . . . . . * hem,htg Fe
[1]3eje.b . . . . . . . . . . . . . . . . . . . . . . . . . . . * hem,htg 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
3ejb.b:zmp
3ejd.b:zmq
3eje.b:zmo
[1] 3ejb.b
0.6
0.6 0.4
[1] 3ejd.b 0.6
0.7
0.4
[1] 3eje.b 0.6 0.8
0.6
[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
3ejb.b
3ejd.b
3eje.b
[1] 3ejb.b
0
0 .01
[1] 3ejd.b 0
0
.01
[1] 3eje.b .01 .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
3ejb.b
3ejd.b
3eje.b
[1] 3ejb.b
0
0.1 0.1
[1] 3ejd.b 0.1
0
0.1
[1] 3eje.b 0.1 0.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.1 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
3ejb.b
3ejd.b
3eje.b
[1] 3ejb.b
0
0.3 0.4
[1] 3ejd.b 0.3
0
0.3
[1] 3eje.b 0.4 0.3
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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

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