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RET4_HUMAN_18_199

Retinol-binding protein 4 [Calycin superfamily. Lipocalin family]

Composition of the binding site

Protein chains monomer
A1 (RET4_HUMAN):47, 50, 53:55, 61, 63, 73:75, 79:82, 89, 91:93, 95, 106, 108, 114:118, 120, 122, 135, 139, 151, 153, 15547, 50, 53:55, 61, 63, 73:75, 79:82, 89, 91:93, 95, 106, 108, 114:118, 120, 122, 135, 139, 151, 153, 155

Full PDB list

1aqb, 1brp, 1brq, 1erb, 1fel, 1fem, 1fen, 1hbp, 1hbq, 1jyd, 1jyj, 1kt3, 1kt4, 1kt5, 1kt6, 1kt7, 1qab, 1rbp, 1rlb, 2wq9, 2wqa, 2wr6, 3bsz, 3fmz, 4o9s, 4psq, 5nty, 5nu2, 5nu6, 5nu7, 5nu8, 5nu9, 5nua, 5nub (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1
K
4
7
P
5
0
L
5
3
F
5
4
L
5
5
A
6
1
F
6
3
A
7
3
T
7
4
A
7
5
V
7
9
R
8
0
L
8
1
L
8
2
M
9
1
V
9
2
G
9
3
F
9
5
M
1
0
6
Y
1
0
8
F
1
1
4
L
1
1
5
Q
1
1
6
G
1
1
8
D
1
2
0
H
1
2
2
Q
1
3
5
R
1
3
9
Y
1
5
1
F
1
5
3
F
1
5
5
[1]1erb.a etr24 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1fel.a fen29 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1fen.a aze20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1jyd.a none . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1kt7.a rtl21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]1rlb.e rea21 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2wq9.a ola20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]2wr6.a odt20 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5nu2.a plm18 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[1]5nua.a dao14 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]3fmz.a 2t128 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4o9s.a 2ry31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
[2]4psq.a 2wl27 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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
K
4
7
P
5
0
L
5
3
F
5
4
L
5
5
A
6
1
F
6
3
A
7
3
T
7
4
A
7
5
V
7
9
R
8
0
L
8
1
L
8
2
A
8
9
M
9
1
V
9
2
G
9
3
F
9
5
M
1
0
6
Y
1
0
8
F
1
1
4
L
1
1
5
Q
1
1
6
K
1
1
7
G
1
1
8
D
1
2
0
H
1
2
2
Q
1
3
5
R
1
3
9
Y
1
5
1
F
1
5
3
F
1
5
5
[1]1erb.a . . . * . . . . . . . . . . . . . . . . . . . * * . . . . . . . .
[1]1fel.a . . . * . . . . . . . . . . . . . . . . . . . * * . . . . . . . .
[1]1fen.a . . . * . . . . . . . . . . . . . . . . . . . * * . . . . . . . .
[1]1jyd.a . . . * . . . . . . . * * . . . . . . . . . . * * . . . . . . . .
[1]1kt7.a . . . * . . . . . . . . . . . . . . . . . . . * * . . . . . . . .
[1]1rlb.e . . . * . . . . . . . . * . . . . . . . . . . * * . . . . . . . .
[1]2wq9.a . . . * . . . . . . . * * . . . . . . . . . . * * . . . . . . . .
[1]2wr6.a . . . * . . . . . . . * * . . . . . . . . . . * * . . . . . . . .
[1]5nu2.a . . . * . . . . . . . . . . . . . . . . . . . * * . . . . . . . .
[1]5nua.a . . . * . . . . . . . . . . . . . . . . . . . * * . . . . . . . .
[2]3fmz.a . . . * . . . . . . . . . . . . . . . . . . . * . . . . . . . . .
[2]4o9s.a . . . * . . . . . . . . * . . . . . . . . * . . . . . . . . . . .
[2]4psq.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
1erb.a:etr
1fel.a:fen
1fen.a:aze
1jyd.a is apo
1kt7.a:rtl
1rlb.e:rea
2wq9.a:ola
2wr6.a:odt
5nu2.a:plm
5nua.a:dao
3fmz.a:2t1
4o9s.a:2ry
4psq.a:2wl
[1] 1erb.a
0
0.4 0 - 0 0 2.7 2.8 3.0 2.8 1.6 2.4 6.3
[1] 1fel.a 0
0.1
0 - 0 0 2.7 2.6 3.1 3.0 1.7 2.3 5.9
[1] 1fen.a 0 0.9
0
- 0 0 2.7 2.7 3.2 3.1 2.3 2.4 6.8
[1] 1jyd.a 4.7 8.1 4.4
-
4.4 4.2 0 0.1 0.1 0.1 5.9 6.3 7.8
[1] 1kt7.a 0.2 1.4 0 -
0
0 2.6 2.5 2.7 2.4 2.1 2.6 6.3
[1] 1rlb.e 0.5 1.7 0.2 - 0.1
0.2
3.1 3.3 3.2 3.3 1.5 2.7 6.2
[1] 2wq9.a 4.4 8.0 4.4 - 4.2 4.2
0
0.1 0 0 5.9 7.0 7.3
[1] 2wr6.a 4.4 7.4 4.4 - 4.3 4.1 0
0.1
0 0 5.7 6.4 7.3
[1] 5nu2.a 4.3 5.0 4.4 - 4.4 4.2 0 0.1
0
0 5.5 6.7 7.7
[1] 5nua.a 4.3 4.7 4.4 - 4.2 4.0 0 0.1 0
0
5.5 7.1 7.5
[2] 3fmz.a 1.0 1.2 0.8 - 0.9 1.2 3.5 3.3 3.5 3.5
0
1.0 3.3
[2] 4o9s.a 0.6 1.5 0.1 - 0.1 0.1 2.8 2.5 2.3 2.6 0.4
0
1.1
[2] 4psq.a 0.7 1.5 0.5 - 0.4 0.5 2.7 2.6 3.2 2.8 0.2 0.9
0
[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
1erb.a
1fel.a
1fen.a
1jyd.a
1kt7.a
1rlb.e
2wq9.a
2wr6.a
5nu2.a
5nua.a
3fmz.a
4o9s.a
4psq.a
[1] 1erb.a
0
.03 .04 .19 .06 .09 .18 .16 .10 .09 .17 .29 .26
[1] 1fel.a .03
0
.06 .21 .08 .08 .20 .18 .12 .11 .17 .28 .23
[1] 1fen.a .04 .06
0
.17 .06 .08 .15 .15 .08 .08 .18 .28 .27
[1] 1jyd.a .19 .21 .17
0
.19 .20 .03 .04 .09 .11 .33 .42 .42
[1] 1kt7.a .06 .08 .06 .19
0
.08 .17 .16 .12 .12 .21 .25 .27
[1] 1rlb.e .09 .08 .08 .20 .08
0
.19 .16 .15 .15 .20 .27 .28
[1] 2wq9.a .18 .20 .15 .03 .17 .19
0
.03 .10 .10 .32 .41 .41
[1] 2wr6.a .16 .18 .15 .04 .16 .16 .03
0
.10 .10 .30 .39 .40
[1] 5nu2.a .10 .12 .08 .09 .12 .15 .10 .10
0
.02 .24 .35 .33
[1] 5nua.a .09 .11 .08 .11 .12 .15 .10 .10 .02
0
.23 .35 .32
[2] 3fmz.a .17 .17 .18 .33 .21 .20 .32 .30 .24 .23
0
.18 .18
[2] 4o9s.a .29 .28 .28 .42 .25 .27 .41 .39 .35 .35 .18
0
.12
[2] 4psq.a .26 .23 .27 .42 .27 .28 .41 .40 .33 .32 .18 .12
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.1 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
1erb.a
1fel.a
1fen.a
1jyd.a
1kt7.a
1rlb.e
2wq9.a
2wr6.a
5nu2.a
5nua.a
3fmz.a
4o9s.a
4psq.a
[1] 1erb.a
0
0.3 0.2 1.0 0.3 0.6 1.0 1.0 0.6 0.6 1.4 1.6 2.9
[1] 1fel.a 0.3
0
0.3 1.2 0.4 0.6 1.2 1.2 0.7 0.7 1.4 1.6 2.9
[1] 1fen.a 0.2 0.3
0
1.1 0.4 0.5 1.1 1.1 0.7 0.7 1.4 1.6 2.9
[1] 1jyd.a 1.0 1.2 1.1
0
1.1 1.0 0.2 0.3 0.9 0.9 1.9 1.8 3.0
[1] 1kt7.a 0.3 0.4 0.4 1.1
0
0.6 1.0 1.1 0.7 0.7 1.5 1.6 2.9
[1] 1rlb.e 0.6 0.6 0.5 1.0 0.6
0
1.1 1.1 0.7 0.7 1.3 1.5 2.6
[1] 2wq9.a 1.0 1.2 1.1 0.2 1.0 1.1
0
0.2 0.9 0.9 1.9 1.9 3.0
[1] 2wr6.a 1.0 1.2 1.1 0.3 1.1 1.1 0.2
0
0.9 0.9 1.9 1.8 3.0
[1] 5nu2.a 0.6 0.7 0.7 0.9 0.7 0.7 0.9 0.9
0
0.1 1.4 1.6 2.8
[1] 5nua.a 0.6 0.7 0.7 0.9 0.7 0.7 0.9 0.9 0.1
0
1.4 1.6 2.8
[2] 3fmz.a 1.4 1.4 1.4 1.9 1.5 1.3 1.9 1.9 1.4 1.4
0
0.9 2.1
[2] 4o9s.a 1.6 1.6 1.6 1.8 1.6 1.5 1.9 1.8 1.6 1.6 0.9
0
1.9
[2] 4psq.a 2.9 2.9 2.9 3.0 2.9 2.6 3.0 3.0 2.8 2.8 2.1 1.9
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.0 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
1erb.a
1fel.a
1fen.a
1jyd.a
1kt7.a
1rlb.e
2wq9.a
2wr6.a
5nu2.a
5nua.a
3fmz.a
4o9s.a
4psq.a
[1] 1erb.a
0
0.7 0.4 2.2 0.7 0.9 2.2 2.2 1.7 1.8 2.0 2.4 3.9
[1] 1fel.a 0.7
0
0.7 2.3 0.8 0.8 2.3 2.3 1.8 1.9 2.0 2.4 3.8
[1] 1fen.a 0.4 0.7
0
2.2 0.6 0.8 2.2 2.2 1.7 1.8 2.0 2.4 3.9
[1] 1jyd.a 2.2 2.3 2.2
0
2.3 2.1 0.5 0.4 1.5 1.5 2.9 3.1 4.0
[1] 1kt7.a 0.7 0.8 0.6 2.3
0
0.8 2.2 2.2 1.8 1.8 2.1 2.5 3.9
[1] 1rlb.e 0.9 0.8 0.8 2.1 0.8
0
2.1 2.1 1.7 1.8 1.9 2.3 3.6
[1] 2wq9.a 2.2 2.3 2.2 0.5 2.2 2.1
0
0.5 1.5 1.4 3.0 3.1 4.1
[1] 2wr6.a 2.2 2.3 2.2 0.4 2.2 2.1 0.5
0
1.4 1.4 2.9 3.1 4.0
[1] 5nu2.a 1.7 1.8 1.7 1.5 1.8 1.7 1.5 1.4
0
0.6 2.5 2.8 3.9
[1] 5nua.a 1.8 1.9 1.8 1.5 1.8 1.8 1.4 1.4 0.6
0
2.6 2.8 4.0
[2] 3fmz.a 2.0 2.0 2.0 2.9 2.1 1.9 3.0 2.9 2.5 2.6
0
1.3 3.0
[2] 4o9s.a 2.4 2.4 2.4 3.1 2.5 2.3 3.1 3.1 2.8 2.8 1.3
0
2.7
[2] 4psq.a 3.9 3.8 3.9 4.0 3.9 3.6 4.1 4.0 3.9 4.0 3.0 2.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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