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CRP_HUMAN_19_224

C-reactive protein [Pentraxin family]

Composition of the binding site

Protein chains monomer [domain annotation]
A1 (CRP_HUMAN):D: Pentraxin (PTX) (79, 82, 84, 86, 92, 99, 156:158, 165, 168)79, 82, 84, 86, 92, 99, 156:158, 165, 168
Metals (Me):Ca

Full PDB list

1b09, 1gnh, 1lj7, 3l2y, 3pvn, 3pvo (redundant Pocketome entry)

Pocket contact map

[download in TSV format]
   
PDB.ch
   
ligand
A1 Me
N
7
9
L
8
2
F
8
4
S
9
2
E
9
9
E
1
5
6
D
1
5
8
Q
1
6
8
[1]1b09.a pc11 . . . . . . . . Ca
[1]3l2y.a ope8 . . . . . . . . Ca
[1]3pvn.b none . . . . . . . . Ca

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 Me
N
7
9
L
8
2
F
8
4
S
8
6
S
9
2
E
9
9
E
1
5
6
Q
1
5
7
D
1
5
8
E
1
6
5
Q
1
6
8
[1]1b09.a . . . . . . . . . . . Ca
[1]3l2y.a . . . . . . . . . . . Ca
[1]3pvn.b . . . . . . . . . . . Ca

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
1b09.a:pc
3l2y.a:ope
3pvn.b is apo
[1] 1b09.a
0
0 -
[1] 3l2y.a 0.1
0
-
[1] 3pvn.b 0.5 0.1
-
[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
1b09.a
3l2y.a
3pvn.b
[1] 1b09.a
0
.01 .05
[1] 3l2y.a .01
0
.04
[1] 3pvn.b .05 .04
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
1b09.a
3l2y.a
3pvn.b
[1] 1b09.a
0
0.3 0.5
[1] 3l2y.a 0.3
0
0.4
[1] 3pvn.b 0.5 0.4
0
[Binding site backbone RMSD matrix]

Site full-atom RMSD (median 0.3 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
1b09.a
3l2y.a
3pvn.b
[1] 1b09.a
0
0.5 0.7
[1] 3l2y.a 0.5
0
0.7
[1] 3pvn.b 0.7 0.7
0
[Binding site full-atom RMSD matrix]







[show 3D visualization]

[ENTRY 2D visualization]

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