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CEAS_STRCL_1_573

N(2)-(2-carboxyethyl)arginine synthase [TPP enzyme family]

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (CEAS_STRCL):R: Thiamine pyrophosphate binding (410:413)
R: Substrate binding (414, 415)
R: Thiamine pyrophosphate binding (436:438)
R: Thiamine pyrophosphate binding (464, 465)
R: Thiamine pyrophosphate binding (490, 492:495)
271, 301, 303, 306, 462, 463, 496, 499, 561, 571, 573
271, 301, 303, 306, 410:415, 436:438, 462:465, 490, 492:496, 499, 561, 571, 573
A2 (CEAS_STRCL):33:36, 57, 80, 83, 84, 87, 120, 12133:36, 57, 80, 83, 84, 87, 120, 121
Metals (Me):Mg

Full PDB list

1upa, 1upb, 1upc, 2iht, 2ihu, 2ihv (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 A2 Me
Y
2
7
1
D
3
0
1
R
3
0
3
M
3
0
6
I
4
1
0
G
4
1
1
F
4
1
2
F
4
1
3
R
4
1
4
H
4
1
5
S
4
3
6
S
4
3
7
F
4
3
8
G
4
6
2
D
4
6
3
G
4
6
4
G
4
6
5
N
4
9
0
T
4
9
2
N
4
9
3
G
4
9
4
L
4
9
5
I
4
9
6
Y
4
9
9
Y
5
6
1
L
5
7
1
I
5
7
3
V
3
3
V
3
4
G
3
5
R
3
6
E
5
7
T
8
0
P
8
3
G
8
4
N
8
7
H
1
2
0
Q
1
2
1
[1]1upb.b tpp26 . . . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . . . . . . . Mg
[1]2iht.b tpp26 . . . * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2ihu.a tar,tp935 . . . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . . . . . . . Mg
[1]2ihu.b tp925 . . . . . . . . . . . . . . . . . . . . . . . . . - - . . . . . . . . . . . Mg
[1]2ihu.c tp8,tp960 . . . . . . . . . . . . . . . . . . . . . . . . . - - . . . . . . . . . . . Mg
[1]2ihv.a gva,tpp37 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 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 A2 Me
Y
2
7
1
D
3
0
1
R
3
0
3
M
3
0
6
I
4
1
0
G
4
1
1
F
4
1
2
F
4
1
3
R
4
1
4
H
4
1
5
S
4
3
6
S
4
3
7
F
4
3
8
G
4
6
2
D
4
6
3
G
4
6
4
G
4
6
5
N
4
9
0
T
4
9
2
N
4
9
3
G
4
9
4
L
4
9
5
I
4
9
6
Y
4
9
9
Y
5
6
1
L
5
7
1
I
5
7
3
V
3
3
V
3
4
G
3
5
R
3
6
E
5
7
T
8
0
P
8
3
G
8
4
N
8
7
H
1
2
0
Q
1
2
1
[1]1upb.b . . . . . . . . . . . . . . . . . . . . . . . . . . - . . . . . . . . . . . Mg
[1]2iht.b . . * * . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mg
[1]2ihu.a . . * . . . . . . . . . . . . . . . . . . . . . . . - . . . . . . . . . . . Mg
[1]2ihu.b . . . . . . . . . . . . . . . . . . . . . . . . . - - . . . . . . . . . . . Mg
[1]2ihu.c . . . . . . . . . . . . . . . . . . . . . . . . . - - . . . . . . . . . . . Mg
[1]2ihv.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

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pocketligand
≥10
9
8
7
6
5
4
3
2
1
0
1upb.b:tpp
2iht.b:tpp
2ihu.a:tar,tp9
2ihu.b:tp9
2ihu.c:tp8,tp9
2ihv.a:gva,tpp
[1] 1upb.b
0.2
0.2 0.3 0.2 0.4 0.8
[1] 2iht.b 0.2
0.2
0.3 0.2 0.6 1.2
[1] 2ihu.a 0.2 0.2
0.2
0.2 0.5 1.1
[1] 2ihu.b 0.1 0.1 0.2
0.2
0.3 0.8
[1] 2ihu.c 0.1 0.1 0.1 0.1
0.4
0.9
[1] 2ihv.a 0.1 0.1 0.2 0.2 0.4
0.1
[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
1upb.b
2iht.b
2ihu.a
2ihu.b
2ihu.c
2ihv.a
[1] 1upb.b
0
.02 .02 .02 .03 .02
[1] 2iht.b .02
0
.01 .02 .02 .03
[1] 2ihu.a .02 .01
0
.01 .01 .03
[1] 2ihu.b .02 .02 .01
0
.01 .03
[1] 2ihu.c .03 .02 .01 .01
0
.04
[1] 2ihv.a .02 .03 .03 .03 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.5 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
1upb.b
2iht.b
2ihu.a
2ihu.b
2ihu.c
2ihv.a
[1] 1upb.b
0
0.1 0.2 0.3 0.5 0.4
[1] 2iht.b 0.1
0
0.2 0.3 0.5 0.4
[1] 2ihu.a 0.2 0.2
0
0.2 0.3 0.3
[1] 2ihu.b 0.3 0.3 0.2
0
0.3 0.3
[1] 2ihu.c 0.5 0.5 0.3 0.3
0
0.4
[1] 2ihv.a 0.4 0.4 0.3 0.3 0.4
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

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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
1upb.b
2iht.b
2ihu.a
2ihu.b
2ihu.c
2ihv.a
[1] 1upb.b
0
0.4 0.4 0.5 0.9 0.7
[1] 2iht.b 0.4
0
0.2 0.3 0.8 0.6
[1] 2ihu.a 0.4 0.2
0
0.2 0.7 0.6
[1] 2ihu.b 0.5 0.3 0.2
0
0.7 0.6
[1] 2ihu.c 0.9 0.8 0.7 0.7
0
1.0
[1] 2ihv.a 0.7 0.6 0.6 0.6 1.0
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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