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CEFE_STRC2_1_311

Deacetoxycephalosporin C synthase [Iron/ascorbate-dependent oxidoreductase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CEFE_STRC2):D: Fe2OG dioxygenase (158, 160, 162, 164, 179, 180, 183, 185, 186, 190, 192, 203, 204, 225, 243, 245, 258, 260, 262, 264)
72:74, 97, 102, 298, 302:305, 307
72:74, 97, 102, 158, 160, 162, 164, 179, 180, 183, 185, 186, 190, 192, 203, 204, 225, 243, 245, 258, 260, 262, 264, 298, 302:305, 307
Metals (Me):Fe

Full PDB list

1dcs, 1e5h, 1e5i, 1hjf, 1hjg, 1rxf, 1rxg, 1unb, 1uo9, 1uob, 1uof, 1uog, 1w28, 1w2a, 1w2n, 1w2o, 2jb8 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
T
7
2
M
7
3
S
1
0
2
L
1
5
8
R
1
6
0
R
1
6
2
M
1
8
0
H
1
8
3
D
1
8
5
T
1
9
0
I
1
9
2
L
2
0
4
H
2
4
3
V
2
4
5
R
2
5
8
S
2
6
0
V
2
6
2
F
2
6
4
N
3
0
4
I
3
0
5
[1]1e5i.a none . . . . . . . . . . . . . . . . . . . . Fe
[1]1hjf.a none . . . . . . . . . . . . . . Q . . . . . Fe
[1]1unb.a pn124 . . . . . . . . . . . . . . . . . . . . Fe
[1]1uob.a pnn23 . . . . . . . . . . . . . . . . . . . . Fe
[1]1w2o.a p1c24 . . . . . . . . . . . . . . . . . . - - Fe
[1]2jb8.a hkv9 . . . . . . . . . . . . . . . . . . . . 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
T
7
2
M
7
3
R
7
4
Y
9
7
S
1
0
2
L
1
5
8
R
1
6
0
R
1
6
2
F
1
6
4
R
1
7
9
M
1
8
0
H
1
8
3
D
1
8
5
L
1
8
6
T
1
9
0
I
1
9
2
S
2
0
3
L
2
0
4
F
2
2
5
H
2
4
3
V
2
4
5
R
2
5
8
S
2
6
0
V
2
6
2
F
2
6
4
I
2
9
8
Y
3
0
2
V
3
0
3
N
3
0
4
I
3
0
5
R
3
0
7
[1]1e5i.a . . . - . . * * . . . . . . . . . . . . . . . . . . . . . . - Fe
[1]1hjf.a . . . . . . * * . . . . . . . . . . . . . Q . . . . . . . . . Fe
[1]1unb.a . . . . . . * * . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]1uob.a . . . . . . * * . . . . . . . . . . . . . . . . . . . . . . . Fe
[1]1w2o.a . . . . . . * . . . . . . . . . . . . . . . . . . . - - - - - Fe
[1]2jb8.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
1e5i.a is apo
1hjf.a is apo
1unb.a:pn1
1uob.a:pnn
1w2o.a:p1c
2jb8.a:hkv
[1] 1e5i.a
-
- 4.4 5.5 2.3 0
[1] 1hjf.a -
-
3.8 5.4 2.3 0
[1] 1unb.a - -
3.5
4.4 1.7 0
[1] 1uob.a - - 3.8
4.4
1.5 0
[1] 1w2o.a - - 1.0 2.5
0
0.1
[1] 2jb8.a - - 3.7 5.1 1.1
0
[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
1e5i.a
1hjf.a
1unb.a
1uob.a
1w2o.a
2jb8.a
[1] 1e5i.a
0
.01 .02 .03 .13 .03
[1] 1hjf.a .01
0
.03 .04 .14 .04
[1] 1unb.a .02 .03
0
.01 .11 .02
[1] 1uob.a .03 .04 .01
0
.10 .02
[1] 1w2o.a .13 .14 .11 .10
0
.10
[1] 2jb8.a .03 .04 .02 .02 .10
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.8 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
1e5i.a
1hjf.a
1unb.a
1uob.a
1w2o.a
2jb8.a
[1] 1e5i.a
0
0.4 0.3 0.3 2.2 0.4
[1] 1hjf.a 0.4
0
0.4 0.4 2.1 0.5
[1] 1unb.a 0.3 0.4
0
0.2 2.2 0.4
[1] 1uob.a 0.3 0.4 0.2
0
2.2 0.4
[1] 1w2o.a 2.2 2.1 2.2 2.2
0
2.0
[1] 2jb8.a 0.4 0.5 0.4 0.4 2.0
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

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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
1e5i.a
1hjf.a
1unb.a
1uob.a
1w2o.a
2jb8.a
[1] 1e5i.a
0
0.6 0.7 0.7 2.9 0.8
[1] 1hjf.a 0.6
0
0.9 1.0 2.7 0.9
[1] 1unb.a 0.7 0.9
0
0.6 2.8 0.9
[1] 1uob.a 0.7 1.0 0.6
0
2.8 0.8
[1] 1w2o.a 2.9 2.7 2.8 2.8
0
2.8
[1] 2jb8.a 0.8 0.9 0.9 0.8 2.8
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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