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PNTM_STRAE_2_398

Pentalenolactone synthase [Cytochrome P450 family]

Composition of the binding site

Protein chains monomer
A1 (PNTM_STRAE):74, 77, 81, 232, 236, 240, 283, 285:287, 387, 38874, 77, 81, 232, 236, 240, 283, 285:287, 387, 388
Cofactors (cF):hem
Metals (Me):Fe

Full PDB list

5l1o, 5l1p, 5l1q, 5l1r, 5l1s, 5l1t, 5l1u, 5l1v, 5l1w

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF Me
R
7
4
M
7
7
M
8
1
F
2
3
2
T
2
3
6
R
2
4
0
N
2
8
3
L
2
8
5
I
2
8
6
P
2
8
7
I
3
8
7
T
3
8
8
[1]5l1o.a 7pf20 . . . . . . . . . . . . hem Fe
[1]5l1p.a 7pt20 . . . . . . . . . . . . hem Fe
[1]5l1q.a 7df20 . . . . . . . . . . . . hem Fe
[1]5l1r.a bcn11 . . . . . . . . . . . . hem Fe
[1]5l1s.a 7pf20 . . . L . . . . . . . . hem Fe
[1]5l1t.a 7pf20 . S . . . . . . . . . . hem Fe
[1]5l1u.a 7pf20 . . A . . . . . . . . . hem Fe
[1]5l1v.a 7pf20 . . C . . . . . . . . . hem Fe
[1]5l1w.a 7pf20 . . * . . . . . . . . . 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
R
7
4
M
7
7
M
8
1
F
2
3
2
T
2
3
6
R
2
4
0
N
2
8
3
L
2
8
5
I
2
8
6
P
2
8
7
I
3
8
7
T
3
8
8
[1]5l1o.a . . . . . . . . . . . . hem Fe
[1]5l1p.a . . . . . . . . . . . . hem Fe
[1]5l1q.a . . . . . . . . . . . . hem Fe
[1]5l1r.a . . . . . . . . . . . . hem Fe
[1]5l1s.a . . . L . . . . . . . . hem Fe
[1]5l1t.a . S . . . . . . . . . . hem Fe
[1]5l1u.a . . A . . . . . . . . . hem Fe
[1]5l1v.a . . C . . . . . . . . . hem Fe
[1]5l1w.a . . * . . . . . . . . . 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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
5l1o.a:7pf
5l1p.a:7pt
5l1q.a:7df
5l1r.a:bcn
5l1s.a:7pf
5l1t.a:7pf
5l1u.a:7pf
5l1v.a:7pf
5l1w.a:7pf
[1] 5l1o.a
0
0 0 0 0 0 0 0 0
[1] 5l1p.a 0
0
0 0 0 0 0 0 0
[1] 5l1q.a 0 0
0
0 0 0 0 0 0
[1] 5l1r.a 0 0 0.2
0
0.1 0.1 0 0 0
[1] 5l1s.a 0 0 0 0
0
0 0 0 0
[1] 5l1t.a 0 0 0 0 0
0
0 0 0
[1] 5l1u.a 0 0 0 0.1 0 0
0
0 0
[1] 5l1v.a 0 0 0 0.1 0 0 0
0
0
[1] 5l1w.a 0 0 0 0.1 0 0 0 0
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
5l1o.a
5l1p.a
5l1q.a
5l1r.a
5l1s.a
5l1t.a
5l1u.a
5l1v.a
5l1w.a
[1] 5l1o.a
0
0 0 .02 0 0 .01 .01 .01
[1] 5l1p.a 0
0
0 .02 0 0 .01 .01 .01
[1] 5l1q.a 0 0
0
.02 0 0 .01 .01 .01
[1] 5l1r.a .02 .02 .02
0
.02 .02 .03 .03 .03
[1] 5l1s.a 0 0 0 .02
0
0 .01 .01 .01
[1] 5l1t.a 0 0 0 .02 0
0
.01 .01 .01
[1] 5l1u.a .01 .01 .01 .03 .01 .01
0
0 0
[1] 5l1v.a .01 .01 .01 .03 .01 .01 0
0
0
[1] 5l1w.a .01 .01 .01 .03 .01 .01 0 0
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.4 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
5l1o.a
5l1p.a
5l1q.a
5l1r.a
5l1s.a
5l1t.a
5l1u.a
5l1v.a
5l1w.a
[1] 5l1o.a
0
0.1 0.1 0.3 0.1 0.1 0.1 0.1 0.1
[1] 5l1p.a 0.1
0
0.1 0.2 0.1 0.2 0.2 0.1 0.1
[1] 5l1q.a 0.1 0.1
0
0.2 0.1 0.1 0.1 0.1 0.1
[1] 5l1r.a 0.3 0.2 0.2
0
0.2 0.2 0.2 0.2 0.3
[1] 5l1s.a 0.1 0.1 0.1 0.2
0
0.1 0.1 0.1 0.1
[1] 5l1t.a 0.1 0.2 0.1 0.2 0.1
0
0.2 0.1 0.1
[1] 5l1u.a 0.1 0.2 0.1 0.2 0.1 0.2
0
0.1 0.1
[1] 5l1v.a 0.1 0.1 0.1 0.2 0.1 0.1 0.1
0
0.1
[1] 5l1w.a 0.1 0.1 0.1 0.3 0.1 0.1 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

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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
5l1o.a
5l1p.a
5l1q.a
5l1r.a
5l1s.a
5l1t.a
5l1u.a
5l1v.a
5l1w.a
[1] 5l1o.a
0
0.6 0.6 0.4 0.1 0.5 0.5 0.1 0.5
[1] 5l1p.a 0.6
0
0.4 0.5 0.5 0.3 0.3 0.6 0.3
[1] 5l1q.a 0.6 0.4
0
0.7 0.5 0.4 0.3 0.6 0.4
[1] 5l1r.a 0.4 0.5 0.7
0
0.4 0.6 0.6 0.4 0.6
[1] 5l1s.a 0.1 0.5 0.5 0.4
0
0.4 0.4 0.1 0.4
[1] 5l1t.a 0.5 0.3 0.4 0.6 0.4
0
0.2 0.5 0.3
[1] 5l1u.a 0.5 0.3 0.3 0.6 0.4 0.2
0
0.5 0.2
[1] 5l1v.a 0.1 0.6 0.6 0.4 0.1 0.5 0.5
0
0.5
[1] 5l1w.a 0.5 0.3 0.4 0.6 0.4 0.3 0.2 0.5
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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