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C1TC_HUMAN_1_305

C-1-tetrahydrofolate synthase, cytoplasmic

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (C1TC_HUMAN):R: Methylenetetrahydrofolate dehydrogenase and cyclohydrolase (52, 55, 56, 98:101, 125, 238, 272:274, 276, 277, 279, 280)
R: Substrate binding (272:274, 276)
52, 55, 56, 98:101, 125, 238, 272:274, 276, 277, 279, 280
Cofactors (cF):nap/ndp

Full PDB list

1a4i, 1dia, 1dib, 1dig

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 cF
Y
5
2
V
5
5
K
5
6
L
9
8
V
9
9
Q
1
0
0
L
1
0
1
D
1
2
5
I
2
3
8
P
2
7
2
G
2
7
3
G
2
7
6
P
2
7
7
T
2
7
9
V
2
8
0
[1]1a4i.a none . . . . . . . . . . . . . . . ndp
[1]1dia.a l2432 . . . . . . . . . . . . . . . nap
[1]1dib.a l3434 . . . . . . . . . . . . . . . nap
[1]1dig.a l3731 . . . . . . . . . . . . . . . nap

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
Y
5
2
V
5
5
K
5
6
L
9
8
V
9
9
Q
1
0
0
L
1
0
1
D
1
2
5
I
2
3
8
P
2
7
2
G
2
7
3
G
2
7
4
G
2
7
6
P
2
7
7
T
2
7
9
V
2
8
0
[1]1a4i.a . . . . . . . . . . . . . . . . ndp
[1]1dia.a . . . . . . . . . . . . . . . . nap
[1]1dib.a . . . . . . . . . . . . . . . . nap
[1]1dig.a . . . . . . . . . . . . . . . . nap

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
1a4i.a is apo
1dia.a:l24
1dib.a:l34
1dig.a:l37
[1] 1a4i.a
-
0.1 0.4 0.3
[1] 1dia.a -
0.1
0.3 0.2
[1] 1dib.a - 0.2
0
0.2
[1] 1dig.a - 0.1 0.3
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
1a4i.a
1dia.a
1dib.a
1dig.a
[1] 1a4i.a
0
.01 .04 .02
[1] 1dia.a .01
0
.02 .01
[1] 1dib.a .04 .02
0
.04
[1] 1dig.a .02 .01 .04
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 0.3 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
1a4i.a
1dia.a
1dib.a
1dig.a
[1] 1a4i.a
0
0.2 0.2 0.1
[1] 1dia.a 0.2
0
0.2 0.1
[1] 1dib.a 0.2 0.2
0
0.2
[1] 1dig.a 0.1 0.1 0.2
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.2 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
1a4i.a
1dia.a
1dib.a
1dig.a
[1] 1a4i.a
0
0.5 0.5 0.5
[1] 1dia.a 0.5
0
0.3 0.1
[1] 1dib.a 0.5 0.3
0
0.2
[1] 1dig.a 0.5 0.1 0.2
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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