1.600 Å
X-ray
2014-12-11
Name: | 5-(hydroxymethyl)furfural oxidase |
---|---|
ID: | HMFO_METS6 |
AC: | E4QP00 |
Organism: | Methylovorus sp. |
Reign: | Bacteria |
TaxID: | 887061 |
EC Number: | / |
Chain Name: | Percentage of Residues within binding site |
---|---|
A | 100 % |
B-Factor: | 11.715 |
---|---|
Number of residues: | 65 |
Including | |
Standard Amino Acids: | 62 |
Non Standard Amino Acids: | 0 |
Water Molecules: | 3 |
Cofactors: | |
Metals: |
Ligandability | Volume (Å3) |
---|---|
0.978 | 675.000 |
% Hydrophobic | % Polar |
---|---|
44.50 | 55.50 |
According to VolSite |
HET Code: | FAD |
---|---|
Formula: | C27H31N9O15P2 |
Molecular weight: | 783.534 g/mol |
DrugBank ID: | DB03147 |
Buried Surface Area: | 78.7 % |
Polar Surface area: | 381.7 Å2 |
Number of | |
---|---|
H-Bond Acceptors: | 22 |
H-Bond Donors: | 7 |
Rings: | 6 |
Aromatic rings: | 3 |
Anionic atoms: | 2 |
Cationic atoms: | 0 |
Rule of Five Violation: | 3 |
Rotatable Bonds: | 13 |
X | Y | Z |
---|---|---|
35.6733 | 13.9151 | 39.0676 |
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 |
O1A | N | THR- 15 | 3.12 | 172.78 | H-Bond (Protein Donor) |
C4' | CB | THR- 15 | 4.29 | 0 | Hydrophobic |
O4' | OG1 | THR- 15 | 3.01 | 173.73 | H-Bond (Ligand Donor) |
O2P | N | ALA- 16 | 2.91 | 169.57 | H-Bond (Protein Donor) |
O3B | OE1 | GLU- 36 | 2.7 | 173.77 | H-Bond (Ligand Donor) |
O2B | OE2 | GLU- 36 | 2.68 | 146.73 | H-Bond (Ligand Donor) |
N3A | N | ALA- 37 | 3.14 | 130.96 | H-Bond (Protein Donor) |
C7M | CD | ARG- 60 | 3.76 | 0 | Hydrophobic |
O2B | NE1 | TRP- 68 | 3.08 | 134.99 | H-Bond (Protein Donor) |
C2B | CZ2 | TRP- 68 | 4 | 0 | Hydrophobic |
C7M | CB | GLU- 90 | 4.15 | 0 | Hydrophobic |
C8M | CB | GLU- 90 | 4.31 | 0 | Hydrophobic |
O1A | N | GLY- 98 | 2.84 | 162.92 | H-Bond (Protein Donor) |
C8M | CG2 | VAL- 101 | 4.12 | 0 | Hydrophobic |
O2' | ND2 | ASN- 102 | 3.13 | 152.3 | H-Bond (Protein Donor) |
C9A | CB | ASN- 102 | 3.35 | 0 | Hydrophobic |
N5 | N | MET- 103 | 3.18 | 176.41 | H-Bond (Protein Donor) |
C6 | CG | MET- 103 | 4.37 | 0 | Hydrophobic |
N3 | O | VAL- 105 | 2.91 | 145.61 | H-Bond (Ligand Donor) |
O4 | N | VAL- 105 | 3.2 | 157.37 | H-Bond (Protein Donor) |
N6A | O | VAL- 233 | 2.85 | 162.03 | H-Bond (Ligand Donor) |
N1A | N | VAL- 233 | 2.99 | 156.07 | H-Bond (Protein Donor) |
C7M | CD2 | TRP- 466 | 3.61 | 0 | Hydrophobic |
C6 | CE3 | TRP- 466 | 3.45 | 0 | Hydrophobic |
C8 | CB | TRP- 466 | 3.29 | 0 | Hydrophobic |
C5' | CB | ALA- 501 | 4.45 | 0 | Hydrophobic |
O1P | N | ALA- 501 | 3.08 | 173.2 | H-Bond (Protein Donor) |
O3' | OG1 | THR- 512 | 2.69 | 169.25 | H-Bond (Protein Donor) |
N1 | N | ASN- 513 | 3.39 | 132.61 | H-Bond (Protein Donor) |
O2 | N | ASN- 513 | 2.75 | 146.62 | H-Bond (Protein Donor) |
C2' | CB | ASN- 513 | 3.82 | 0 | Hydrophobic |
C5' | CG2 | THR- 516 | 4.16 | 0 | Hydrophobic |
O2P | O | HOH- 2007 | 2.76 | 173.38 | H-Bond (Protein Donor) |
O2 | O | HOH- 2111 | 2.63 | 179.95 | H-Bond (Protein Donor) |