2.460 Å
X-ray
2014-02-17
Name: | Peptidoglycan recognition protein 1 |
---|---|
ID: | PGRP1_CAMDR |
AC: | Q9GK12 |
Organism: | Camelus dromedarius |
Reign: | Eukaryota |
TaxID: | 9838 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 10 % |
C | 47 % |
D | 43 % |
B-Factor: | 37.390 |
---|---|
Number of residues: | 50 |
Including | |
Standard Amino Acids: | 49 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 1 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
1.329 | 1171.125 |
% Hydrophobic | % Polar |
---|---|
43.23 | 56.77 |
According to VolSite |
HET Code: | LP5 |
---|---|
Formula: | C34H64NO12P |
Molecular weight: | 709.845 g/mol |
DrugBank ID: | - |
Buried Surface Area: | 61.66 % |
Polar Surface area: | 227.77 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 12 |
H-Bond Donors: | 5 |
Rings: | 1 |
Aromatic rings: | 0 |
Anionic atoms: | 2 |
Cationic atoms: | 0 |
Rule of Five Violation: | 2 |
Rotatable Bonds: | 30 |
X | Y | Z |
---|---|---|
-30.001 | -28.3665 | -21.4612 |
Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand
Ligand | Protein | Interaction | |||
---|---|---|---|---|---|
Atom | Atom | Residue | Distance (Å) | Angle (°) | Type |
C1 | CE2 | TRP- 66 | 4.21 | 0 | Hydrophobic |
C29 | CH2 | TRP- 66 | 3.63 | 0 | Hydrophobic |
C39 | CH2 | TRP- 66 | 4.1 | 0 | Hydrophobic |
C41 | CZ2 | TRP- 66 | 4.49 | 0 | Hydrophobic |
O44 | NE1 | TRP- 66 | 2.75 | 157.46 | H-Bond (Protein Donor) |
C6 | CD | LYS- 90 | 4.3 | 0 | Hydrophobic |
O6 | O | GLY- 91 | 3.11 | 126.82 | H-Bond (Ligand Donor) |
C1 | CB | ALA- 92 | 4.08 | 0 | Hydrophobic |
C4 | CB | ALA- 92 | 4.18 | 0 | Hydrophobic |
C39 | CB | ALA- 92 | 4.03 | 0 | Hydrophobic |
O42 | N | GLY- 95 | 2.96 | 137.02 | H-Bond (Protein Donor) |
C41 | CG | PRO- 96 | 4.19 | 0 | Hydrophobic |
C3 | CG | PRO- 96 | 3.99 | 0 | Hydrophobic |
C18 | CG2 | THR- 97 | 4.2 | 0 | Hydrophobic |
C8 | CB | THR- 97 | 3.69 | 0 | Hydrophobic |
C18 | CE2 | TRP- 98 | 4.29 | 0 | Hydrophobic |
C22 | CZ2 | TRP- 98 | 4.25 | 0 | Hydrophobic |
C26 | CH2 | TRP- 98 | 3.89 | 0 | Hydrophobic |
C20 | CZ2 | TRP- 98 | 3.69 | 0 | Hydrophobic |
C24 | CH2 | TRP- 98 | 4.14 | 0 | Hydrophobic |
O42 | ND2 | ASN- 99 | 3.05 | 157.77 | H-Bond (Protein Donor) |
C27 | CB | SER- 139 | 3.93 | 0 | Hydrophobic |
C18 | CB | ASN- 140 | 3.89 | 0 | Hydrophobic |
C24 | CD | LYS- 144 | 4.08 | 0 | Hydrophobic |
O44 | O | VAL- 149 | 2.52 | 169.65 | H-Bond (Ligand Donor) |
C20 | CG1 | VAL- 149 | 3.86 | 0 | Hydrophobic |
O7 | NE2 | GLN- 150 | 2.65 | 133.11 | H-Bond (Protein Donor) |
O43 | OE1 | GLN- 150 | 2.94 | 172.93 | H-Bond (Ligand Donor) |
C31 | CB | GLN- 150 | 4.43 | 0 | Hydrophobic |
C33 | CB | GLN- 150 | 4.09 | 0 | Hydrophobic |
C35 | CG | GLN- 150 | 3.88 | 0 | Hydrophobic |
C31 | CG | PRO- 151 | 3.8 | 0 | Hydrophobic |
C36 | CG | PRO- 151 | 4.02 | 0 | Hydrophobic |