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COFD_METMA_1_303

2-phospho-L-lactate transferase [CofD family]

Composition of the binding site

Protein chains monomer
A1 (COFD_METMA):6:9, 12, 191:193, 197, 220, 221, 227:232, 284:2866:9, 12, 191:193, 197, 220, 221, 227:232, 284:286
Cofactors (cF):fo1

Full PDB list

3c3d, 3c3e, 3cgw (redundant Pocketome entry)

Pocket contact map

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PDB.ch
   
ligand
A1 cF
G
6
G
7
T
8
G
9
P
1
9
1
S
1
9
2
N
1
9
3
S
1
9
7
S
2
2
0
P
2
2
1
P
2
2
7
V
2
2
8
S
2
2
9
T
2
8
4
M
2
8
6
[1]3c3d.d none . . . . . . . . . . . . . . * fo1
[1]3c3e.a gdp28 . . . . . . . . . . . . . . * fo1

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

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PDB.ch
A1 cF
G
6
G
7
T
8
G
9
K
1
2
P
1
9
1
S
1
9
2
N
1
9
3
S
1
9
7
S
2
2
0
P
2
2
1
P
2
2
7
V
2
2
8
S
2
2
9
G
2
3
0
P
2
3
1
A
2
3
2
T
2
8
4
L
2
8
5
M
2
8
6
[1]3c3d.d . * . . . . . . . . . . . . . . . . . * fo1
[1]3c3e.a . . . . . . . . . . . . . . . . . . . * fo1

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
3c3d.d is apo
3c3e.a:gdp
[1] 3c3d.d
-
2.5
[1] 3c3e.a -
0.2
[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
3c3d.d
3c3e.a
[1] 3c3d.d
0
.11
[1] 3c3e.a .11
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
3c3d.d
3c3e.a
[1] 3c3d.d
0
0.9
[1] 3c3e.a 0.9
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
3c3d.d
3c3e.a
[1] 3c3d.d
0
0.9
[1] 3c3e.a 0.9
0
[Binding site full-atom RMSD matrix]







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[ENTRY 2D visualization]

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