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ENO1_YEAST_2_437

Enolase 1 [Enolase family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (ENO1_YEAST):R: Substrate binding (373:376)
37:41, 160, 168, 169, 212, 247, 296, 321, 322, 344, 346, 397
37:41, 160, 168, 169, 212, 247, 296, 321, 322, 344, 346, 373:376, 397
Metals (Me):Mg/Mn/Zn

Full PDB list

1ebg, 1ebh, 1els, 1l8p, 1nel, 1one, 1p43, 1p48, 2al1, 2al2, 2one, 2xgz, 2xh0, 2xh2, 2xh4, 2xh7, 3enl, 4enl, 5enl, 6enl, 7enl (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
G
3
8
A
3
9
S
4
0
T
4
1
H
1
6
0
Q
1
6
8
E
1
6
9
E
2
1
2
D
2
4
7
E
2
9
6
D
3
2
1
D
3
2
2
L
3
4
4
K
3
4
6
S
3
7
3
H
3
7
4
R
3
7
5
S
3
7
6
K
3
9
7
[1]1ebg.a mg,pah10 . . . . . . . . . . . . . . . . . . . Mg
[1]1els.a mn,pah10 . . . . . . . . . . . . . . . . . . . Mn
[1]1l8p.b mg,pah10 . . A . . . . . . . . . . . . . . . . Mg
[1]1nel.a none . . . . . . . . . . . . . . . . . . . Mg
[1]1p43.a 2pg,mg12 . . . . . . Q . . . . . . . . . . . . Mg
[1]1p48.a mg,pep11 . . . . . . . Q . . . . . . . . . . . Mg
[1]2al1.a 2pg,mg,pep22 . . . . . . . . . . . . . . . . . . . Mg
[1]2al1.b mg,pep11 . . . . - . . . . . . . . . . . . . . Mg
[1]2al2.a 2pg,mg,pep22 . . . . . . . . . . . . . A . . . . . Mg
[1]2one.a 2pg,li12 . . . . . . . . . . . . . . . . . . . Mg
[1]2one.b pep10 . . . . . . . . . . . . . . . . . . . Mg
[1]2xgz.a pep10 . . N . . . . . . . . R . . . . . . . Mg
[1]2xh0.b pep10 . . N . . K . . . . . R . . . . . . . Mg
[1]2xh2.a 2pg11 . . N . . . . . . . . A . . . . . . . Mg
[1]2xh4.a 2pg11 . . A . . . . . . . . A . . . . . . . Mg
[1]2xh4.d 2pg11 . - - - . . . . . . . A . . . . . . . Mg
[1]2xh7.a 2pg,mg12 . . . . . . . . . . . A . . . . . . . Mg
[1]6enl.a pga9 . . . . . . . . . . . . . . . . . . . Zn
[1]7enl.a 2pg11 . . . . . . . . . . . . . . . . . . . Mg

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
S
3
7
G
3
8
A
3
9
S
4
0
T
4
1
H
1
6
0
Q
1
6
8
E
1
6
9
E
2
1
2
D
2
4
7
E
2
9
6
D
3
2
1
D
3
2
2
L
3
4
4
K
3
4
6
S
3
7
3
H
3
7
4
R
3
7
5
S
3
7
6
K
3
9
7
[1]1ebg.a . . . * . . . . . . . . . . . . . . . . Mg
[1]1els.a . . . . . . . . . . . . . . . . . . . . Mn
[1]1l8p.b . . . A . . . . . . . . . . . . . . . . Mg
[1]1nel.a . . . . . . . . . . . . . . . . . . . . Mg
[1]1p43.a . . . . . . . Q . . . . . . . . . . . . Mg
[1]1p48.a . . . * . . . . Q . . . . . . . . . . . Mg
[1]2al1.a . . . * . . . . . . . . . . . . . . . . Mg
[1]2al1.b . . . * . - . . . . . . . . . . . . . . Mg
[1]2al2.a . . . * . . . . . . . . . . A . . . . . Mg
[1]2one.a . . . * . . . . . . . . . . . . . . . . Mg
[1]2one.b . . . * . . . . . . . . . . . . . . . . Mg
[1]2xgz.a . . . N . . . . . . . . R . . . . . . . Mg
[1]2xh0.b . . . N . . K . . . . . R . . . . . . . Mg
[1]2xh2.a . . . N . . . . . . . . A . . . . . . . Mg
[1]2xh4.a . . . A . . . . . . . . A . . . . . . . Mg
[1]2xh4.d . . - - - . . . . . . . A . . . . . . . Mg
[1]2xh7.a . . . * . . . . . . . . A . . . . . . . Mg
[1]6enl.a . . . . . . . . . . . . . . . . . . . . Zn
[1]7enl.a . . . . . . . . . . . . . . . . . . . . Mg

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
1ebg.a:mg,pah
1els.a:mn,pah
1l8p.b:mg,pah
1nel.a is apo
1p43.a:2pg,mg
1p48.a:mg,pep
2al1.a:2pg,mg,pep
2al1.b:mg,pep
2al2.a:2pg,mg,pep
2one.a:2pg,li
2one.b:pep
2xgz.a:pep
2xh0.b:pep
2xh2.a:2pg
2xh4.a:2pg
2xh4.d:2pg
2xh7.a:2pg,mg
6enl.a:pga
7enl.a:2pg
[1] 1ebg.a
0.3
1.2 0.3 - 0.9 0.2 0.3 0.3 0.3 0.3 0.3 0.2 0.1 0.4 0.3 0.1 0.3 0.8 0.2
[1] 1els.a 0.1
0.2
0.1 - 0.4 0.1 0.2 0.1 0.3 0.1 0 0 0 0.2 0.4 0 0.1 0 0.3
[1] 1l8p.b 0.1 0.9
0
- 0.3 0 0.2 0.1 0.2 0.2 0.3 0.1 0 0.4 0.4 0.3 0.2 0.7 0.3
[1] 1nel.a 0.2 0.8 0.3
-
0.5 0.3 0.3 0.3 0.2 0.1 0.1 0 0 0.1 0.4 0.1 0.2 0.5 0.2
[1] 1p43.a 0.1 0.9 0.1 -
0.2
0 0.2 0.1 0.2 0.2 0.2 0.1 0 0.3 0.4 0.1 0.3 0.5 0.2
[1] 1p48.a 0.1 1.0 0.2 - 0.7
0.2
0.1 0.2 0.3 0.2 0.3 0.1 0.1 0.4 0.2 0.2 0.2 0.6 0.2
[1] 2al1.a 0.5 1.3 0.6 - 1.3 0.6
0.2
0.3 0.3 0.3 0.3 0.1 0.1 0.3 0.5 0.1 0.3 0.7 0.4
[1] 2al1.b 0.6 1.1 0.3 - 1.0 0.4 0.2
0.2
0.5 0.3 0.3 0.1 0 0.1 0.3 0.1 0.3 0.8 0.2
[1] 2al2.a 0.6 1.1 0.8 - 1.8 0.8 0.5 0.5
0.3
0.4 0.3 0.1 0.2 0.6 0.5 0.2 0.6 1.2 0.7
[1] 2one.a 0.8 1.0 0.6 - 2.0 0.8 0.5 0.5 0.7
0.5
0.3 0.2 0.2 0.5 0.4 0.1 0.5 1.1 0.5
[1] 2one.b 0.6 1.0 0.7 - 0.9 0.8 0.5 0.6 0.6 0.4
0.3
0.2 0.3 0.2 0.2 0.3 0.5 0.8 0.4
[1] 2xgz.a 1.0 1.0 0.9 - 1.7 0.9 1.1 0.9 1.1 0.5 0.1
0
0 0.1 0.3 0.1 0.9 0.5 0.5
[1] 2xh0.b 1.1 1.0 1.2 - 1.5 0.9 1.0 0.7 0.9 0.8 0.2 0
0
0.4 0.2 0.2 0.8 0.6 0.2
[1] 2xh2.a 0.1 0.8 0.1 - 0 0 0.1 0 0.2 0.1 0.2 0 0
0
0.3 0 0.1 0.6 0.1
[1] 2xh4.a 0.4 1.2 0.6 - 1.2 0.2 0.1 0.2 0.1 0.4 0.3 0.1 0.1 0.1
0.3
0.1 0.1 0.7 0.3
[1] 2xh4.d 0 0.9 0 - 0.2 0 0.2 0 0 0.3 0.1 0 0.1 0.3 0.3
0.1
0.2 0.5 0.2
[1] 2xh7.a 0.4 1.2 0.5 - 1.0 0.4 0.2 0.2 0.2 0.3 0.3 0.1 0.1 0.3 0.5 0.1
0.3
0.6 0.6
[1] 6enl.a 0 0.4 0 - 0 0 0 0 0.1 0 0.1 0 0 0 0.3 0.1 0
0
0.1
[1] 7enl.a 0.2 0.9 0.1 - 0.3 0.1 0.1 0.1 0.2 0.3 0.2 0.1 0.1 0.2 0.3 0 0.2 0.5
0.1
[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
1ebg.a
1els.a
1l8p.b
1nel.a
1p43.a
1p48.a
2al1.a
2al1.b
2al2.a
2one.a
2one.b
2xgz.a
2xh0.b
2xh2.a
2xh4.a
2xh4.d
2xh7.a
6enl.a
7enl.a
[1] 1ebg.a
0
.11 .10 .12 .11 .06 .08 .06 .08 .06 .07 .19 .16 .10 .08 .08 .06 .17 .12
[1] 1els.a .11
0
.08 .07 .06 .08 .14 .10 .16 .15 .08 .15 .16 .06 .12 .07 .12 .06 .07
[1] 1l8p.b .10 .08
0
.08 .04 .08 .12 .10 .14 .13 .11 .13 .12 .04 .10 .06 .11 .09 .09
[1] 1nel.a .12 .07 .08
0
.06 .08 .10 .09 .13 .14 .07 .15 .16 .07 .10 .10 .09 .09 .08
[1] 1p43.a .11 .06 .04 .06
0
.08 .12 .09 .16 .14 .08 .12 .11 .03 .10 .06 .11 .06 .06
[1] 1p48.a .06 .08 .08 .08 .08
0
.07 .05 .10 .08 .07 .14 .13 .06 .07 .07 .06 .12 .10
[1] 2al1.a .08 .14 .12 .10 .12 .07
0
.06 .06 .06 .09 .19 .17 .12 .07 .12 .06 .15 .14
[1] 2al1.b .06 .10 .10 .09 .09 .05 .06
0
.10 .08 .05 .15 .18 .08 .06 .12 .09 .13 .11
[1] 2al2.a .08 .16 .14 .13 .16 .10 .06 .10
0
.04 .11 .23 .20 .15 .07 .12 .05 .21 .16
[1] 2one.a .06 .15 .13 .14 .14 .08 .06 .08 .04
0
.10 .22 .18 .14 .06 .10 .06 .19 .16
[1] 2one.b .07 .08 .11 .07 .08 .07 .09 .05 .11 .10
0
.17 .18 .08 .09 .12 .09 .13 .07
[1] 2xgz.a .19 .15 .13 .15 .12 .14 .19 .15 .23 .22 .17
0
.06 .10 .19 .14 .18 .15 .15
[1] 2xh0.b .16 .16 .12 .16 .11 .13 .17 .18 .20 .18 .18 .06
0
.10 .15 .09 .15 .15 .14
[1] 2xh2.a .10 .06 .04 .07 .03 .06 .12 .08 .15 .14 .08 .10 .10
0
.10 .05 .10 .07 .06
[1] 2xh4.a .08 .12 .10 .10 .10 .07 .07 .06 .07 .06 .09 .19 .15 .10
0
.10 .04 .14 .13
[1] 2xh4.d .08 .07 .06 .10 .06 .07 .12 .12 .12 .10 .12 .14 .09 .05 .10
0
.08 .09 .08
[1] 2xh7.a .06 .12 .11 .09 .11 .06 .06 .09 .05 .06 .09 .18 .15 .10 .04 .08
0
.16 .14
[1] 6enl.a .17 .06 .09 .09 .06 .12 .15 .13 .21 .19 .13 .15 .15 .07 .14 .09 .16
0
.07
[1] 7enl.a .12 .07 .09 .08 .06 .10 .14 .11 .16 .16 .07 .15 .14 .06 .13 .08 .14 .07
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.2 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
1ebg.a
1els.a
1l8p.b
1nel.a
1p43.a
1p48.a
2al1.a
2al1.b
2al2.a
2one.a
2one.b
2xgz.a
2xh0.b
2xh2.a
2xh4.a
2xh4.d
2xh7.a
6enl.a
7enl.a
[1] 1ebg.a
0
1.3 0.9 0.7 1.1 0.7 0.2 0.3 0.2 0.3 1.2 1.1 1.1 1.1 0.2 0.3 0.2 3.9 1.6
[1] 1els.a 1.3
0
1.0 1.2 0.9 1.1 1.3 0.9 1.3 1.3 0.8 1.0 1.1 0.9 1.3 1.2 1.3 3.6 1.3
[1] 1l8p.b 0.9 1.0
0
1.0 0.5 1.0 1.0 0.7 1.0 1.0 0.9 0.5 0.7 0.4 1.0 0.8 1.0 3.5 1.2
[1] 1nel.a 0.7 1.2 1.0
0
1.2 1.0 0.7 0.7 0.7 0.7 1.2 1.2 1.2 1.2 0.7 0.5 0.7 4.0 1.6
[1] 1p43.a 1.1 0.9 0.5 1.2
0
1.0 1.1 0.5 1.1 1.1 0.7 0.6 0.8 0.5 1.1 1.1 1.1 3.5 1.2
[1] 1p48.a 0.7 1.1 1.0 1.0 1.0
0
0.7 0.2 0.7 0.8 1.1 0.9 0.8 1.0 0.7 0.8 0.7 3.9 1.5
[1] 2al1.a 0.2 1.3 1.0 0.7 1.1 0.7
0
0.2 0.2 0.2 1.2 1.1 1.2 1.2 0.2 0.3 0.1 4.0 1.6
[1] 2al1.b 0.3 0.9 0.7 0.7 0.5 0.2 0.2
0
0.3 0.3 0.6 0.8 0.7 0.7 0.3 0.4 0.3 4.0 1.4
[1] 2al2.a 0.2 1.3 1.0 0.7 1.1 0.7 0.2 0.3
0
0.2 1.2 1.1 1.2 1.2 0.1 0.3 0.2 4.0 1.6
[1] 2one.a 0.3 1.3 1.0 0.7 1.1 0.8 0.2 0.3 0.2
0
1.2 1.2 1.3 1.2 0.2 0.3 0.2 4.0 1.7
[1] 2one.b 1.2 0.8 0.9 1.2 0.7 1.1 1.2 0.6 1.2 1.2
0
1.0 1.1 0.9 1.1 1.2 1.1 3.8 1.2
[1] 2xgz.a 1.1 1.0 0.5 1.2 0.6 0.9 1.1 0.8 1.1 1.2 1.0
0
0.4 0.4 1.1 1.0 1.1 3.4 1.2
[1] 2xh0.b 1.1 1.1 0.7 1.2 0.8 0.8 1.2 0.7 1.2 1.3 1.1 0.4
0
0.5 1.2 1.1 1.2 3.6 1.2
[1] 2xh2.a 1.1 0.9 0.4 1.2 0.5 1.0 1.2 0.7 1.2 1.2 0.9 0.4 0.5
0
1.2 1.1 1.2 3.5 1.2
[1] 2xh4.a 0.2 1.3 1.0 0.7 1.1 0.7 0.2 0.3 0.1 0.2 1.1 1.1 1.2 1.2
0
0.3 0.1 4.0 1.6
[1] 2xh4.d 0.3 1.2 0.8 0.5 1.1 0.8 0.3 0.4 0.3 0.3 1.2 1.0 1.1 1.1 0.3
0
0.3 1.6 1.2
[1] 2xh7.a 0.2 1.3 1.0 0.7 1.1 0.7 0.1 0.3 0.2 0.2 1.1 1.1 1.2 1.2 0.1 0.3
0
4.0 1.6
[1] 6enl.a 3.9 3.6 3.5 4.0 3.5 3.9 4.0 4.0 4.0 4.0 3.8 3.4 3.6 3.5 4.0 1.6 4.0
0
3.1
[1] 7enl.a 1.6 1.3 1.2 1.6 1.2 1.5 1.6 1.4 1.6 1.7 1.2 1.2 1.2 1.2 1.6 1.2 1.6 3.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
1ebg.a
1els.a
1l8p.b
1nel.a
1p43.a
1p48.a
2al1.a
2al1.b
2al2.a
2one.a
2one.b
2xgz.a
2xh0.b
2xh2.a
2xh4.a
2xh4.d
2xh7.a
6enl.a
7enl.a
[1] 1ebg.a
0
1.4 0.9 0.8 1.2 1.4 0.3 0.4 0.4 0.5 1.2 1.0 1.6 1.3 0.3 0.5 0.3 3.6 1.9
[1] 1els.a 1.4
0
1.1 1.3 1.0 1.5 1.4 1.0 1.4 1.4 1.0 1.1 1.4 1.1 1.4 1.3 1.4 3.3 1.7
[1] 1l8p.b 0.9 1.1
0
1.1 0.5 1.4 1.0 0.7 1.1 1.1 1.0 0.5 1.2 0.7 1.0 0.9 1.0 3.1 1.4
[1] 1nel.a 0.8 1.3 1.1
0
1.3 1.6 0.8 0.8 0.8 0.9 1.3 1.1 1.8 1.4 0.8 0.7 0.8 3.6 1.9
[1] 1p43.a 1.2 1.0 0.5 1.3
0
1.4 1.2 0.7 1.3 1.3 0.9 0.6 1.2 0.7 1.2 1.1 1.2 3.2 1.6
[1] 1p48.a 1.4 1.5 1.4 1.6 1.4
0
1.5 0.4 1.5 1.5 1.6 0.8 0.8 1.4 1.4 1.5 1.5 3.7 2.1
[1] 2al1.a 0.3 1.4 1.0 0.8 1.2 1.5
0
0.2 0.2 0.5 1.3 1.1 1.7 1.3 0.3 0.5 0.3 3.7 1.9
[1] 2al1.b 0.4 1.0 0.7 0.8 0.7 0.4 0.2
0
0.3 0.5 0.8 0.7 0.6 0.8 0.4 0.5 0.4 3.6 1.6
[1] 2al2.a 0.4 1.4 1.1 0.8 1.3 1.5 0.2 0.3
0
0.5 1.4 1.1 1.7 1.4 0.3 0.5 0.3 3.7 2.0
[1] 2one.a 0.5 1.4 1.1 0.9 1.3 1.5 0.5 0.5 0.5
0
1.3 1.1 1.8 1.4 0.4 0.6 0.4 3.7 2.0
[1] 2one.b 1.2 1.0 1.0 1.3 0.9 1.6 1.3 0.8 1.4 1.3
0
1.0 1.5 1.1 1.3 1.2 1.3 3.5 1.6
[1] 2xgz.a 1.0 1.1 0.5 1.1 0.6 0.8 1.1 0.7 1.1 1.1 1.0
0
0.5 0.7 1.0 0.9 1.0 3.0 1.4
[1] 2xh0.b 1.6 1.4 1.2 1.8 1.2 0.8 1.7 0.6 1.7 1.8 1.5 0.5
0
1.1 1.7 1.7 1.7 3.3 1.8
[1] 2xh2.a 1.3 1.1 0.7 1.4 0.7 1.4 1.3 0.8 1.4 1.4 1.1 0.7 1.1
0
1.4 1.3 1.4 3.1 1.6
[1] 2xh4.a 0.3 1.4 1.0 0.8 1.2 1.4 0.3 0.4 0.3 0.4 1.3 1.0 1.7 1.4
0
0.4 0.2 3.5 1.8
[1] 2xh4.d 0.5 1.3 0.9 0.7 1.1 1.5 0.5 0.5 0.5 0.6 1.2 0.9 1.7 1.3 0.4
0
0.4 1.5 1.4
[1] 2xh7.a 0.3 1.4 1.0 0.8 1.2 1.5 0.3 0.4 0.3 0.4 1.3 1.0 1.7 1.4 0.2 0.4
0
3.7 1.9
[1] 6enl.a 3.6 3.3 3.1 3.6 3.2 3.7 3.7 3.6 3.7 3.7 3.5 3.0 3.3 3.1 3.5 1.5 3.7
0
2.9
[1] 7enl.a 1.9 1.7 1.4 1.9 1.6 2.1 1.9 1.6 2.0 2.0 1.6 1.4 1.8 1.6 1.8 1.4 1.9 2.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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