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CNX1_ARATH_462_626

Molybdopterin biosynthesis protein CNX1

Composition of the binding site

Protein chains homodimer [domain annotation]
A1 (CNX1_ARATH):R: MPT adenylyltransferase (473, 478, 484:487, 540:543, 548, 573, 577, 579, 580, 582, 583, 599:601, 604, 607)
R: Substrate binding (542, 543)
473, 478, 484:487, 540:543, 548, 573, 577, 579, 580, 582, 583, 599:601, 604, 607
A2 (CNX1_ARATH):R: MPT adenylyltransferase (618)
622
618, 622

Full PDB list

1eav, 1o8n, 1o8o, 1o8q, 1uux, 1uuy

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
T
4
7
3
V
4
7
8
P
4
8
4
D
4
8
5
R
4
8
6
S
4
8
7
G
5
4
0
G
5
4
1
T
5
4
2
G
5
4
3
D
5
4
8
S
5
7
3
T
5
7
7
F
5
7
9
A
5
8
0
L
5
8
2
S
5
8
3
P
5
9
9
G
6
0
0
N
6
0
1
A
6
0
4
E
6
0
7
[1]1eav.c none . . . . . . . . . . . . . . . . . . . . . .
[1]1o8n.a none . . . . . . . . A . . . . . . . . . . . . .
[1]1o8o.a none . . . . . . . . D . . . . . . . . . . . . .
[1]1o8q.d none . . . . . . . . . . . A . . . . . . . . . .
[1]1uux.a cu1,mte25 . . . . . . . . . . . . . . . . . . . . . .
[1]1uuy.a cu1,mte.amp47 . . . . . . . . . . . . . . . . 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 A2
T
4
7
3
V
4
7
8
P
4
8
4
D
4
8
5
R
4
8
6
S
4
8
7
G
5
4
0
G
5
4
1
T
5
4
2
G
5
4
3
D
5
4
8
S
5
7
3
T
5
7
7
F
5
7
9
A
5
8
0
L
5
8
2
S
5
8
3
P
5
9
9
G
6
0
0
N
6
0
1
A
6
0
4
E
6
0
7
H
6
1
8
Q
6
2
2
[1]1eav.c . . . . . . . . . . . . . . . . . . . . . . . .
[1]1o8n.a . . . . . . . . A . . . . . . . . . . . . . . .
[1]1o8o.a . . . . . . . . D . . . . . . . . . . . . . . .
[1]1o8q.d . . . . . . . . . . . A . . . . . . . . . . . .
[1]1uux.a . . . . . . . . . . . . . . . . . . . . . . - -
[1]1uuy.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
1eav.c is apo
1o8n.a is apo
1o8o.a is apo
1o8q.d is apo
1uux.a:cu1,mte
1uuy.a:cu1,mte.amp
[1] 1eav.c
-
- - - 0.2 0.2
[1] 1o8n.a -
-
- - 0.1 0.1
[1] 1o8o.a - -
-
- 0.7 0.9
[1] 1o8q.d - - -
-
0.1 0.2
[1] 1uux.a - - - -
0
0
[1] 1uuy.a - - - - 0.1
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
1eav.c
1o8n.a
1o8o.a
1o8q.d
1uux.a
1uuy.a
[1] 1eav.c
0
0 .03 .01 .01 .01
[1] 1o8n.a 0
0
.03 .01 0 .01
[1] 1o8o.a .03 .03
0
.03 .04 .04
[1] 1o8q.d .01 .01 .03
0
.01 .01
[1] 1uux.a .01 0 .04 .01
0
0
[1] 1uuy.a .01 .01 .04 .01 0
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

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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
1eav.c
1o8n.a
1o8o.a
1o8q.d
1uux.a
1uuy.a
[1] 1eav.c
0
0.4 0.5 0.3 0.6 0.6
[1] 1o8n.a 0.4
0
0.2 0.4 0.4 0.4
[1] 1o8o.a 0.5 0.2
0
0.4 0.4 0.4
[1] 1o8q.d 0.3 0.4 0.4
0
0.5 0.5
[1] 1uux.a 0.6 0.4 0.4 0.5
0
0.1
[1] 1uuy.a 0.6 0.4 0.4 0.5 0.1
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
1eav.c
1o8n.a
1o8o.a
1o8q.d
1uux.a
1uuy.a
[1] 1eav.c
0
0.5 0.6 0.4 0.9 0.9
[1] 1o8n.a 0.5
0
0.4 0.5 0.8 0.8
[1] 1o8o.a 0.6 0.4
0
0.6 0.8 0.8
[1] 1o8q.d 0.4 0.5 0.6
0
0.9 0.8
[1] 1uux.a 0.9 0.8 0.8 0.9
0
0.2
[1] 1uuy.a 0.9 0.8 0.8 0.8 0.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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