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5NTC_HUMAN_1_536

Cytosolic purine 5'-nucleotidase [5'(3')-deoxyribonucleotidase family]

Composition of the binding site

Protein chains monomer
A1 (5NTC_HUMAN):8:15, 27, 57, 59, 227, 229, 231, 376, 463, 464, 4668:15, 27, 57, 59, 227, 229, 231, 376, 463, 464, 466
Metals (Me):Mg

Full PDB list

2j2c, 2jc9, 2jcm, 2xcv, 2xcw, 2xcx, 2xjb, 2xjc, 2xjd, 2xje, 2xjf, 4h4b, 5cqz, 5cr7, 5k7y, 5l4z, 5l50 (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
L
5
7
V
5
9
V
2
2
7
S
4
6
4
I
4
6
6
[1]2xjf.a none . . . . .
[1]5cr7.b 5wo10 . . . . . Mg

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
R
8
L
9
Q
1
0
N
1
1
A
1
2
A
1
3
D
1
4
M
1
5
Y
2
7
L
5
7
V
5
9
V
2
2
7
D
2
2
9
K
2
3
1
A
3
7
6
A
4
6
3
S
4
6
4
I
4
6
6
[1]2xjf.a . . . . . . . . . . . . . . . . . .
[1]5cr7.b - - - - - - - - . . . . . . . . . . Mg

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
2xjf.a is apo
5cr7.b:5wo
[1] 2xjf.a
-
0.1
[1] 5cr7.b -
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
2xjf.a
5cr7.b
[1] 2xjf.a
0
.01
[1] 5cr7.b .01
0
[Pocket clash dissimilarity matrix]

Site backbone RMSD (median 2.4 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
2xjf.a
5cr7.b
[1] 2xjf.a
0
3.6
[1] 5cr7.b 3.6
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 1.8 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
2xjf.a
5cr7.b
[1] 2xjf.a
0
4.9
[1] 5cr7.b 4.9
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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