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B4GT1_HUMAN_125_398

Beta-1,4-galactosyltransferase 1 [Glycosyltransferase 7 family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (B4GT1_HUMAN):R: UDP-alpha-D-galactose binding (183:185, 187)
R: UDP-alpha-D-galactose binding (222, 224)
R: UDP-alpha-D-galactose binding (249, 250)
R: N-acetyl-D-glucosamine binding (312:315)
R: UDP-alpha-D-galactose binding (343:346)
248, 251, 273, 275, 276, 281, 282, 285, 287, 288, 310, 311, 340, 342, 349, 351:356, 359
183:185, 187, 222, 224, 248:251, 273, 275, 276, 281, 282, 285, 287, 288, 310:315, 340, 342:346, 349, 351:356, 359
Metals (Me):Mn

Full PDB list

1nf5, 1nkh, 1nqi, 1nwg, 1o23, 1oqm, 2ae7, 2aec, 2aes, 2agd, 2ah9, 2fy7, 2fya, 2fyb, 3ee5, 4ee3, 4ee4, 4ee5, 4eea, 4eeg, 4eem, 4eeo, 4l41 (redundant Pocketome entry); 1nhe (unprocessed)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
P
1
8
3
F
1
8
4
R
1
8
5
R
1
8
7
F
2
2
2
R
2
2
4
D
2
4
8
V
2
4
9
D
2
5
0
L
2
5
1
M
2
7
3
K
2
7
5
F
2
7
6
P
2
8
1
Y
2
8
2
Y
2
8
5
G
2
8
7
G
2
8
8
W
3
1
0
G
3
1
1
G
3
1
2
E
3
1
3
D
3
1
4
D
3
1
5
M
3
4
0
R
3
4
2
H
3
4
3
R
3
4
5
D
3
4
6
N
3
4
9
R
3
5
5
F
3
5
6
I
3
5
9
[1]1nf5.b CVLFH42 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1nkh.b CVLFH-C,pg4,udp86 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]1nqi.d CVLFH-C48 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1nwg.d bgn,CVLFH-C65 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1o23.b CVLFH-C,upg84 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]1o23.d CVLFH,upg78 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]1oqm.b CVLFH,ud281 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]1oqm.d CVLFH-C,ud287 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]2agd.c udh32 . . . . . . . . . . . . . . . . . . . . . . . . H . . . . . . . . Mn
[1]2ah9.b cto,udh75 . . . . . . . . . . . . . . . . . . . . . . . . H . . . . . . . . Mn
[1]4ee4.c udp25 . . . . . . . . . . . . . . . . . . . . . . . . H . . . . . . . . Mn
[1]4l41.c LICTMFH58 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]2fy7.a none . . . . . . . . . . . . . . . . . . . . . . . . H . - - - - . . .

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
P
1
8
3
F
1
8
4
R
1
8
5
R
1
8
7
F
2
2
2
R
2
2
4
D
2
4
8
V
2
4
9
D
2
5
0
L
2
5
1
M
2
7
3
K
2
7
5
F
2
7
6
P
2
8
1
Y
2
8
2
Y
2
8
5
G
2
8
7
G
2
8
8
W
3
1
0
G
3
1
1
G
3
1
2
E
3
1
3
D
3
1
4
D
3
1
5
M
3
4
0
R
3
4
2
H
3
4
3
S
3
4
4
R
3
4
5
D
3
4
6
N
3
4
9
P
3
5
1
N
3
5
2
P
3
5
3
Q
3
5
4
R
3
5
5
F
3
5
6
I
3
5
9
[1]1nf5.b . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . * . .
[1]1nkh.b . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . Mn
[1]1nqi.d . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . .
[1]1nwg.d . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . .
[1]1o23.b . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . Mn
[1]1o23.d . . . . . . . . . . . . . . . * . . . . . . . . . . . . . . . . . . . . . . Mn
[1]1oqm.b . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Mn
[1]1oqm.d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * . Mn
[1]2agd.c . . . . . . . . . . . . . . . * . . . . . . . . H . . . . . . . . . . . . . Mn
[1]2ah9.b . . . . . . . . . . . . . . . * . . . . . . . . H . . . . . . . . . . . . . Mn
[1]4ee4.c . . . . . . . . . . . . . . . * . . . . . . . . H . . . . . . . . . . . . . Mn
[1]4l41.c . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . * .
[2]2fy7.a . . . . . . . . . . . . . . . . . . . . . . . . H . - - - - - - * * * * * .

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
1nf5.b:CVLFH
1nkh.b:CVLFH-C,pg4,udp
1nqi.d:CVLFH-C
1nwg.d:CVLFH-C,bgn
1o23.b:CVLFH-C,upg
1o23.d:CVLFH,upg
1oqm.b:CVLFH,ud2
1oqm.d:CVLFH-C,ud2
2agd.c:udh
2ah9.b:cto,udh
4ee4.c:udp
4l41.c:LICTMFH
2fy7.a is apo
[1] 1nf5.b
0
0.4 0 1.5 0.3 0.7 0.3 1.4 0.2 1.4 0.3 0 -
[1] 1nkh.b 0
0.1
0 0.6 0.3 0.5 0.6 1.4 0.3 0.3 0.2 0 -
[1] 1nqi.d 0 0.4
0
0.5 1.0 0.9 0.9 1.6 0.6 0.6 0.3 0 -
[1] 1nwg.d 0 0.4 0
0
0.7 0.9 0.6 1.5 0.2 0.3 0.3 0 -
[1] 1o23.b 0 0.3 0 0.9
0.3
0.1 0.5 1.3 0.4 0.8 0.2 0 -
[1] 1o23.d 0 0.3 0.1 0.9 0.2
0.1
0.7 1.3 0.3 0.7 0.1 0 -
[1] 1oqm.b 0 0.1 0.1 0.9 0.5 0.2
0
0.6 0.6 0.9 0.1 0 -
[1] 1oqm.d 0 0.2 0 1.3 0.5 0.2 0.3
0.2
0.3 0.7 0.1 0 -
[1] 2agd.c 0 0.2 0.2 0.5 0.2 0.2 0.4 1.3
0
0.1 0 0 -
[1] 2ah9.b 0 0.2 0.1 0.6 0.2 0.2 0.4 1.3 0.1
0
0 0 -
[1] 4ee4.c 0 0.1 0.2 0.6 0.1 0.2 0.4 1.3 0 0
0.1
0 -
[1] 4l41.c 0 0.4 0.2 1.7 0.5 0.8 0.9 1.4 0.6 1.0 0.1
0
-
[2] 2fy7.a 9.9 11 11 15 10 11 9.8 11 0.1 12 0.1 7.5
-
[Pocket-ligand steric clashes matrix]

Pocket clash dissimilarity (2 clusters)

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
1nf5.b
1nkh.b
1nqi.d
1nwg.d
1o23.b
1o23.d
1oqm.b
1oqm.d
2agd.c
2ah9.b
4ee4.c
4l41.c
2fy7.a
[1] 1nf5.b
0
.07 .07 .06 .07 .08 .08 .10 .06 .06 .06 .09 .43
[1] 1nkh.b .07
0
.06 .06 .02 .03 .06 .06 .05 .04 .04 .06 .49
[1] 1nqi.d .07 .06
0
.04 .06 .05 .09 .08 .06 .06 .06 .09 .49
[1] 1nwg.d .06 .06 .04
0
.06 .05 .07 .07 .04 .03 .04 .09 .48
[1] 1o23.b .07 .02 .06 .06
0
.02 .05 .06 .04 .04 .04 .06 .49
[1] 1o23.d .08 .03 .05 .05 .02
0
.06 .05 .04 .04 .03 .07 .49
[1] 1oqm.b .08 .06 .09 .07 .05 .06
0
.03 .06 .06 .06 .06 .46
[1] 1oqm.d .10 .06 .08 .07 .06 .05 .03
0
.07 .07 .07 .05 .46
[1] 2agd.c .06 .05 .06 .04 .04 .04 .06 .07
0
.01 .01 .07 .48
[1] 2ah9.b .06 .04 .06 .03 .04 .04 .06 .07 .01
0
.01 .07 .48
[1] 4ee4.c .06 .04 .06 .04 .04 .03 .06 .07 .01 .01
0
.07 .47
[1] 4l41.c .09 .06 .09 .09 .06 .07 .06 .05 .07 .07 .07
0
.47
[2] 2fy7.a .43 .49 .49 .48 .49 .49 .46 .46 .48 .48 .47 .47
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 1.0 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
1nf5.b
1nkh.b
1nqi.d
1nwg.d
1o23.b
1o23.d
1oqm.b
1oqm.d
2agd.c
2ah9.b
4ee4.c
4l41.c
2fy7.a
[1] 1nf5.b
0
0.6 0.5 0.5 0.6 0.6 0.5 0.6 0.5 0.5 0.5 0.4 5.2
[1] 1nkh.b 0.6
0
0.5 0.6 0.2 0.3 0.3 0.4 0.5 0.5 0.6 0.7 5.2
[1] 1nqi.d 0.5 0.5
0
0.2 0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 5.2
[1] 1nwg.d 0.5 0.6 0.2
0
0.5 0.5 0.5 0.5 0.5 0.5 0.5 0.5 5.2
[1] 1o23.b 0.6 0.2 0.5 0.5
0
0.2 0.3 0.3 0.5 0.5 0.5 0.6 5.2
[1] 1o23.d 0.6 0.3 0.5 0.5 0.2
0
0.3 0.4 0.4 0.4 0.5 0.6 5.2
[1] 1oqm.b 0.5 0.3 0.5 0.5 0.3 0.3
0
0.3 0.4 0.4 0.5 0.5 5.2
[1] 1oqm.d 0.6 0.4 0.5 0.5 0.3 0.4 0.3
0
0.5 0.5 0.6 0.5 5.1
[1] 2agd.c 0.5 0.5 0.5 0.5 0.5 0.4 0.4 0.5
0
0.2 0.2 0.5 5.2
[1] 2ah9.b 0.5 0.5 0.5 0.5 0.5 0.4 0.4 0.5 0.2
0
0.2 0.5 5.2
[1] 4ee4.c 0.5 0.6 0.5 0.5 0.5 0.5 0.5 0.6 0.2 0.2
0
0.5 5.2
[1] 4l41.c 0.4 0.7 0.5 0.5 0.6 0.6 0.5 0.5 0.5 0.5 0.5
0
5.1
[2] 2fy7.a 5.2 5.2 5.2 5.2 5.2 5.2 5.2 5.1 5.2 5.2 5.2 5.1
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.5 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
1nf5.b
1nkh.b
1nqi.d
1nwg.d
1o23.b
1o23.d
1oqm.b
1oqm.d
2agd.c
2ah9.b
4ee4.c
4l41.c
2fy7.a
[1] 1nf5.b
0
0.9 0.9 1.0 1.0 1.2 1.2 1.0 1.1 1.2 1.1 1.3 6.2
[1] 1nkh.b 0.9
0
1.0 1.0 0.3 0.8 0.9 0.7 1.1 1.1 1.2 1.4 6.3
[1] 1nqi.d 0.9 1.0
0
0.4 1.0 1.1 1.1 0.9 0.9 1.3 1.0 1.5 6.4
[1] 1nwg.d 1.0 1.0 0.4
0
1.0 1.1 1.1 0.9 0.9 1.3 0.9 1.5 6.4
[1] 1o23.b 1.0 0.3 1.0 1.0
0
0.7 0.9 0.7 1.1 1.1 1.2 1.4 6.3
[1] 1o23.d 1.2 0.8 1.1 1.1 0.7
0
0.6 0.9 1.0 0.9 1.2 1.3 6.4
[1] 1oqm.b 1.2 0.9 1.1 1.1 0.9 0.6
0
0.8 1.0 1.0 1.1 1.3 6.3
[1] 1oqm.d 1.0 0.7 0.9 0.9 0.7 0.9 0.8
0
0.9 1.2 1.0 1.4 6.3
[1] 2agd.c 1.1 1.1 0.9 0.9 1.1 1.0 1.0 0.9
0
0.9 0.5 1.3 6.3
[1] 2ah9.b 1.2 1.1 1.3 1.3 1.1 0.9 1.0 1.2 0.9
0
1.0 1.0 6.3
[1] 4ee4.c 1.1 1.2 1.0 0.9 1.2 1.2 1.1 1.0 0.5 1.0
0
1.3 6.3
[1] 4l41.c 1.3 1.4 1.5 1.5 1.4 1.3 1.3 1.4 1.3 1.0 1.3
0
6.2
[2] 2fy7.a 6.2 6.3 6.4 6.4 6.3 6.4 6.3 6.3 6.3 6.3 6.3 6.2
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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