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DFPA_LOLVU_2_314

Diisopropyl-fluorophosphatase

Composition of the binding site

Protein chains monomer
A1 (DFPA_LOLVU):21, 36:39, 74, 90, 120, 121, 146, 148, 175, 195, 229, 244, 271, 28721, 36:39, 74, 90, 120, 121, 146, 148, 175, 195, 229, 244, 271, 287
Metals (Me):Ca

Full PDB list

1e1a, 1pjx, 2gvu, 2gvv, 2gvw, 2gvx, 2iao, 2iap, 2iaq, 2iar, 2ias, 2iat, 2iau, 2iav, 2iaw, 2iax, 3byc, 3hlh, 3hli, 3i1c, 3kgg, 3li3, 3li4, 3li5, 3o4p, 3u0s (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
E
2
1
P
3
6
A
7
4
M
9
0
N
1
2
0
N
1
7
5
D
2
2
9
W
2
4
4
S
2
7
1
H
2
8
7
[1]1pjx.a none . . . . . . . . . . Ca
[1]2gvu.a none . . . . D . N . . . Ca
[1]2gvv.a di915 . . . . . . . . . . Ca
[1]2gvx.a none . . . . . D N . . . Ca
[1]2iao.a none . . . . . . . . . . Ca
[1]2iap.a none Q . . . . . . . . . Ca
[1]2iaq.a none . . . . . . . . A . Ca
[1]2iar.a none . . . . . . . H . . Ca
[1]2ias.a none . . . . . . . F . . Ca
[1]2iat.a none . . . . . . . L . . Ca
[1]2iau.a none . . . . . . . Y . . Ca
[1]2iav.a none . . . . . . . . . A Ca
[1]2iaw.a none . . . . . D . . . . Ca
[1]3hlh.b none . . . . . . . . . . Ca
[1]3hli.c none . . . . . . . . . . Ca
[1]3i1c.a none A . I . A A A . . .
[1]3li3.a none . . . . . . . . . . Ca
[1]3li4.a none . . . . D D N . . . Ca
[1]3li5.a none Q . . . D D N . . . Ca
[1]3u0s.a none T S I . A A A . A .

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
E
2
1
P
3
6
E
3
7
V
3
8
E
3
9
.
3
9
D
A
7
4
M
9
0
N
1
2
0
D
1
2
1
R
1
4
6
M
1
4
8
N
1
7
5
T
1
9
5
D
2
2
9
W
2
4
4
S
2
7
1
H
2
8
7
[1]1pjx.a . . . . . - . . . . . . . . . . . . Ca
[1]2gvu.a . . . . . - . . D . . . . . N . . . Ca
[1]2gvv.a . . . . . - . . . . . . . . . . . . Ca
[1]2gvx.a . . . . . - . . . . . . D . N . . . Ca
[1]2iao.a . . Q . . - . . . . . . . . . . . . Ca
[1]2iap.a Q . . . . - . . . . . . . . . . . . Ca
[1]2iaq.a . . . . . - . . . . . . . . . . A . Ca
[1]2iar.a . . . . . - . . . . . . . . . H . . Ca
[1]2ias.a . . . . . - . . . . . . . . . F . . Ca
[1]2iat.a . . . . . - . . . . . . . . . L . . Ca
[1]2iau.a . . . . . - . . . . . . . . . Y . . Ca
[1]2iav.a . . . . . - . . . . . . . . . . . A Ca
[1]2iaw.a . . . . . - . . . . . . D . . . . . Ca
[1]3hlh.b . . A . . - . . . . A . . M . . . . Ca
[1]3hli.c . . D . . - . . . . A . . M . . . . Ca
[1]3i1c.a A . Y . . - I . A Y I L A Q A . . .
[1]3li3.a . . . . . - . . . E . . . . . . . . Ca
[1]3li4.a . . . . . - . . D . . . D . N . . . Ca
[1]3li5.a Q . . . . - . . D . . . D . N . . . Ca
[1]3u0s.a T S P L S T I . A Y I L A Q A . A .

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
1pjx.a is apo
2gvu.a is apo
2gvv.a:di9
2gvx.a is apo
2iao.a is apo
2iap.a is apo
2iaq.a is apo
2iar.a is apo
2ias.a is apo
2iat.a is apo
2iau.a is apo
2iav.a is apo
2iaw.a is apo
3hlh.b is apo
3hli.c is apo
3i1c.a is apo
3li3.a is apo
3li4.a is apo
3li5.a is apo
3u0s.a is apo
[1] 1pjx.a
-
- 0.2 - - - - - - - - - - - - - - - - -
[1] 2gvu.a -
-
0.1 - - - - - - - - - - - - - - - - -
[1] 2gvv.a - -
0
- - - - - - - - - - - - - - - - -
[1] 2gvx.a - - 0
-
- - - - - - - - - - - - - - - -
[1] 2iao.a - - 0 -
-
- - - - - - - - - - - - - - -
[1] 2iap.a - - 0.3 - -
-
- - - - - - - - - - - - - -
[1] 2iaq.a - - 0 - - -
-
- - - - - - - - - - - - -
[1] 2iar.a - - 0 - - - -
-
- - - - - - - - - - - -
[1] 2ias.a - - 0 - - - - -
-
- - - - - - - - - - -
[1] 2iat.a - - 0 - - - - - -
-
- - - - - - - - - -
[1] 2iau.a - - 0.1 - - - - - - -
-
- - - - - - - - -
[1] 2iav.a - - 0 - - - - - - - -
-
- - - - - - - -
[1] 2iaw.a - - 0 - - - - - - - - -
-
- - - - - - -
[1] 3hlh.b - - 0.4 - - - - - - - - - -
-
- - - - - -
[1] 3hli.c - - 0.4 - - - - - - - - - - -
-
- - - - -
[1] 3i1c.a - - 1.1 - - - - - - - - - - - -
-
- - - -
[1] 3li3.a - - 0 - - - - - - - - - - - - -
-
- - -
[1] 3li4.a - - 0.2 - - - - - - - - - - - - - -
-
- -
[1] 3li5.a - - 0.5 - - - - - - - - - - - - - - -
-
-
[1] 3u0s.a - - 2.7 - - - - - - - - - - - - - - - -
-
[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
1pjx.a
2gvu.a
2gvv.a
2gvx.a
2iao.a
2iap.a
2iaq.a
2iar.a
2ias.a
2iat.a
2iau.a
2iav.a
2iaw.a
3hlh.b
3hli.c
3i1c.a
3li3.a
3li4.a
3li5.a
3u0s.a
[1] 1pjx.a
0
.01 .01 .01 .01 .03 .01 .01 .01 .01 .02 .01 .01 .03 .03 .06 .01 .01 .03 .16
[1] 2gvu.a .01
0
.01 .01 .01 .02 .01 .01 .01 .01 .01 .01 .01 .03 .03 .07 .01 .01 .02 .16
[1] 2gvv.a .01 .01
0
0 0 .02 0 0 0 0 .01 0 0 .02 .02 .06 0 .01 .03 .15
[1] 2gvx.a .01 .01 0
0
0 .02 0 0 0 0 .01 0 0 .02 .02 .06 0 .01 .03 .15
[1] 2iao.a .01 .01 0 0
0
.02 0 0 0 0 .01 0 0 .02 .02 .06 0 .01 .03 .15
[1] 2iap.a .03 .02 .02 .02 .02
0
.02 .02 .02 .02 .01 .02 .02 .04 .04 .08 .02 .02 .01 .17
[1] 2iaq.a .01 .01 0 0 0 .02
0
0 0 0 .01 0 0 .02 .02 .06 0 .01 .03 .15
[1] 2iar.a .01 .01 0 0 0 .02 0
0
0 0 .01 0 0 .02 .02 .06 0 .01 .03 .15
[1] 2ias.a .01 .01 0 0 0 .02 0 0
0
0 .01 0 0 .02 .02 .06 0 .01 .03 .15
[1] 2iat.a .01 .01 0 0 0 .02 0 0 0
0
.01 0 0 .02 .02 .06 0 .01 .03 .15
[1] 2iau.a .02 .01 .01 .01 .01 .01 .01 .01 .01 .01
0
.01 .01 .03 .03 .07 .01 .01 .02 .16
[1] 2iav.a .01 .01 0 0 0 .02 0 0 0 0 .01
0
0 .02 .02 .06 0 .01 .03 .15
[1] 2iaw.a .01 .01 0 0 0 .02 0 0 0 0 .01 0
0
.02 .02 .06 0 .01 .03 .15
[1] 3hlh.b .03 .03 .02 .02 .02 .04 .02 .02 .02 .02 .03 .02 .02
0
0 .06 .02 .03 .05 .14
[1] 3hli.c .03 .03 .02 .02 .02 .04 .02 .02 .02 .02 .03 .02 .02 0
0
.06 .02 .03 .05 .14
[1] 3i1c.a .06 .07 .06 .06 .06 .08 .06 .06 .06 .06 .07 .06 .06 .06 .06
0
.06 .07 .09 .12
[1] 3li3.a .01 .01 0 0 0 .02 0 0 0 0 .01 0 0 .02 .02 .06
0
.01 .03 .15
[1] 3li4.a .01 .01 .01 .01 .01 .02 .01 .01 .01 .01 .01 .01 .01 .03 .03 .07 .01
0
.02 .16
[1] 3li5.a .03 .02 .03 .03 .03 .01 .03 .03 .03 .03 .02 .03 .03 .05 .05 .09 .03 .02
0
.18
[1] 3u0s.a .16 .16 .15 .15 .15 .17 .15 .15 .15 .15 .16 .15 .15 .14 .14 .12 .15 .16 .18
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.6 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
1pjx.a
2gvu.a
2gvv.a
2gvx.a
2iao.a
2iap.a
2iaq.a
2iar.a
2ias.a
2iat.a
2iau.a
2iav.a
2iaw.a
3hlh.b
3hli.c
3i1c.a
3li3.a
3li4.a
3li5.a
3u0s.a
[1] 1pjx.a
0
0.3 0.3 0.4 0.3 0.4 0.2 0.1 0.2 0.2 0.3 0.3 0.3 0.3 0.4 0.7 0.2 0.3 0.3 3.1
[1] 2gvu.a 0.3
0
0.2 0.2 0.2 0.2 0.3 0.3 0.2 0.3 0.2 0.2 0.2 0.4 0.3 0.4 0.2 0.2 0.2 3.3
[1] 2gvv.a 0.3 0.2
0
0.3 0.1 0.3 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.3 0.3 0.5 0.1 0.2 0.3 3.2
[1] 2gvx.a 0.4 0.2 0.3
0
0.3 0.3 0.4 0.4 0.3 0.3 0.3 0.2 0.2 0.5 0.4 0.4 0.4 0.2 0.3 3.4
[1] 2iao.a 0.3 0.2 0.1 0.3
0
0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.5 0.2 0.2 0.3 3.3
[1] 2iap.a 0.4 0.2 0.3 0.3 0.2
0
0.3 0.3 0.3 0.3 0.2 0.2 0.3 0.4 0.3 0.5 0.3 0.2 0.2 3.3
[1] 2iaq.a 0.2 0.3 0.2 0.4 0.2 0.3
0
0.1 0.1 0.2 0.2 0.2 0.2 0.3 0.3 0.6 0.2 0.2 0.3 3.2
[1] 2iar.a 0.1 0.3 0.2 0.4 0.2 0.3 0.1
0
0.1 0.1 0.2 0.2 0.3 0.3 0.3 0.6 0.2 0.2 0.3 3.2
[1] 2ias.a 0.2 0.2 0.2 0.3 0.2 0.3 0.1 0.1
0
0.1 0.2 0.2 0.2 0.3 0.3 0.6 0.2 0.2 0.3 3.2
[1] 2iat.a 0.2 0.3 0.2 0.3 0.2 0.3 0.2 0.1 0.1
0
0.2 0.2 0.3 0.4 0.4 0.6 0.2 0.2 0.3 3.2
[1] 2iau.a 0.3 0.2 0.2 0.3 0.2 0.2 0.2 0.2 0.2 0.2
0
0.2 0.2 0.4 0.3 0.5 0.3 0.2 0.3 3.3
[1] 2iav.a 0.3 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2
0
0.2 0.4 0.3 0.5 0.2 0.1 0.2 3.3
[1] 2iaw.a 0.3 0.2 0.2 0.2 0.2 0.3 0.2 0.3 0.2 0.3 0.2 0.2
0
0.3 0.3 0.5 0.2 0.1 0.2 3.2
[1] 3hlh.b 0.3 0.4 0.3 0.5 0.4 0.4 0.3 0.3 0.3 0.4 0.4 0.4 0.3
0
0.3 0.7 0.3 0.3 0.4 3.1
[1] 3hli.c 0.4 0.3 0.3 0.4 0.3 0.3 0.3 0.3 0.3 0.4 0.3 0.3 0.3 0.3
0
0.6 0.3 0.3 0.3 3.2
[1] 3i1c.a 0.7 0.4 0.5 0.4 0.5 0.5 0.6 0.6 0.6 0.6 0.5 0.5 0.5 0.7 0.6
0
0.6 0.5 0.5 3.5
[1] 3li3.a 0.2 0.2 0.1 0.4 0.2 0.3 0.2 0.2 0.2 0.2 0.3 0.2 0.2 0.3 0.3 0.6
0
0.2 0.3 3.2
[1] 3li4.a 0.3 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.2 0.1 0.1 0.3 0.3 0.5 0.2
0
0.2 3.3
[1] 3li5.a 0.3 0.2 0.3 0.3 0.3 0.2 0.3 0.3 0.3 0.3 0.3 0.2 0.2 0.4 0.3 0.5 0.3 0.2
0
3.3
[1] 3u0s.a 3.1 3.3 3.2 3.4 3.3 3.3 3.2 3.2 3.2 3.2 3.3 3.3 3.2 3.1 3.2 3.5 3.2 3.3 3.3
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1pjx.a
2gvu.a
2gvv.a
2gvx.a
2iao.a
2iap.a
2iaq.a
2iar.a
2ias.a
2iat.a
2iau.a
2iav.a
2iaw.a
3hlh.b
3hli.c
3i1c.a
3li3.a
3li4.a
3li5.a
3u0s.a
[1] 1pjx.a
0
0.8 0.8 0.8 0.5 0.7 0.5 0.4 0.6 0.4 0.6 0.8 0.6 0.5 0.5 0.9 0.6 0.6 0.9 3.0
[1] 2gvu.a 0.8
0
0.3 0.6 0.6 0.7 0.6 0.7 0.7 0.7 0.6 0.9 0.4 0.5 0.5 0.5 0.5 0.5 0.8 3.1
[1] 2gvv.a 0.8 0.3
0
0.5 0.5 0.8 0.6 0.7 0.7 0.6 0.7 0.8 0.5 0.5 0.5 0.7 0.5 0.5 0.8 3.1
[1] 2gvx.a 0.8 0.6 0.5
0
0.6 0.8 0.7 0.7 0.8 0.7 0.8 0.7 0.5 0.6 0.5 0.5 0.6 0.5 0.7 3.2
[1] 2iao.a 0.5 0.6 0.5 0.6
0
0.6 0.3 0.3 0.4 0.3 0.3 0.8 0.5 0.6 0.5 0.7 0.5 0.5 0.8 3.1
[1] 2iap.a 0.7 0.7 0.8 0.8 0.6
0
0.6 0.6 0.7 0.6 0.6 0.9 0.7 0.7 0.7 0.7 0.7 0.7 0.7 3.2
[1] 2iaq.a 0.5 0.6 0.6 0.7 0.3 0.6
0
0.4 0.4 0.3 0.4 0.9 0.5 0.5 0.5 0.8 0.5 0.6 0.9 3.0
[1] 2iar.a 0.4 0.7 0.7 0.7 0.3 0.6 0.4
0
0.3 0.3 0.5 0.9 0.6 0.6 0.6 0.9 0.6 0.6 0.9 3.2
[1] 2ias.a 0.6 0.7 0.7 0.8 0.4 0.7 0.4 0.3
0
0.4 0.5 1.0 0.6 0.6 0.6 0.9 0.6 0.7 1.0 3.2
[1] 2iat.a 0.4 0.7 0.6 0.7 0.3 0.6 0.3 0.3 0.4
0
0.4 0.8 0.5 0.6 0.6 0.8 0.5 0.5 0.9 3.2
[1] 2iau.a 0.6 0.6 0.7 0.8 0.3 0.6 0.4 0.5 0.5 0.4
0
0.9 0.6 0.6 0.5 0.7 0.5 0.7 0.9 3.2
[1] 2iav.a 0.8 0.9 0.8 0.7 0.8 0.9 0.9 0.9 1.0 0.8 0.9
0
0.8 0.4 0.4 0.6 0.8 0.7 0.9 3.2
[1] 2iaw.a 0.6 0.4 0.5 0.5 0.5 0.7 0.5 0.6 0.6 0.5 0.6 0.8
0
0.4 0.4 0.6 0.4 0.4 0.8 3.1
[1] 3hlh.b 0.5 0.5 0.5 0.6 0.6 0.7 0.5 0.6 0.6 0.6 0.6 0.4 0.4
0
0.3 0.8 0.4 0.4 0.7 2.9
[1] 3hli.c 0.5 0.5 0.5 0.5 0.5 0.7 0.5 0.6 0.6 0.6 0.5 0.4 0.4 0.3
0
0.7 0.5 0.4 0.7 3.0
[1] 3i1c.a 0.9 0.5 0.7 0.5 0.7 0.7 0.8 0.9 0.9 0.8 0.7 0.6 0.6 0.8 0.7
0
0.7 0.6 0.6 3.0
[1] 3li3.a 0.6 0.5 0.5 0.6 0.5 0.7 0.5 0.6 0.6 0.5 0.5 0.8 0.4 0.4 0.5 0.7
0
0.6 0.9 3.1
[1] 3li4.a 0.6 0.5 0.5 0.5 0.5 0.7 0.6 0.6 0.7 0.5 0.7 0.7 0.4 0.4 0.4 0.6 0.6
0
0.7 3.1
[1] 3li5.a 0.9 0.8 0.8 0.7 0.8 0.7 0.9 0.9 1.0 0.9 0.9 0.9 0.8 0.7 0.7 0.6 0.9 0.7
0
3.1
[1] 3u0s.a 3.0 3.1 3.1 3.2 3.1 3.2 3.0 3.2 3.2 3.2 3.2 3.2 3.1 2.9 3.0 3.0 3.1 3.1 3.1
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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