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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

3w4y

2.000 Å

X-ray

2013-01-17

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Mitochondrial FAD-linked sulfhydryl oxidase ERV1
ID:ERV1_YEAST
AC:P27882
Organism:Saccharomyces cerevisiae
Reign:Eukaryota
TaxID:559292
EC Number:1.8.3.2


Chains:

Chain Name:Percentage of Residues
within binding site
A13 %
B87 %


Ligand binding site composition:

B-Factor:11.201
Number of residues:48
Including
Standard Amino Acids: 46
Non Standard Amino Acids: 1
Water Molecules: 1
Cofactors: FAD
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.0941005.750

% Hydrophobic% Polar
56.0443.96
According to VolSite

Ligand :
3w4y_2 Structure
HET Code: FAD
Formula: C27H31N9O15P2
Molecular weight: 783.534 g/mol
DrugBank ID: DB03147
Buried Surface Area:68.05 %
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

Mass center Coordinates

XYZ
-2.80810.552237.58


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

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

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
C5'CGGLU- 883.770Hydrophobic
C5'CBARG- 924.460Hydrophobic
O2PNH2ARG- 923.02146.69H-Bond
(Protein Donor)
O2PNEARG- 923.2141.17H-Bond
(Protein Donor)
O2PCZARG- 923.550Ionic
(Protein Cationic)
C8MCBSER- 943.870Hydrophobic
C7MCH2TRP- 953.850Hydrophobic
C8MCE2TRP- 953.230Hydrophobic
C8CZ2TRP- 953.410Hydrophobic
O2'NE1TRP- 952.87175.71H-Bond
(Protein Donor)
C7MCD1LEU- 984.470Hydrophobic
C8MCD1LEU- 984.110Hydrophobic
C7MCE1PHE- 1244.270Hydrophobic
C8MCZTYR- 1283.930Hydrophobic
C6CBCYS- 1333.920Hydrophobic
C9ASGCYS- 1334.20Hydrophobic
C7MCGPHE- 1373.840Hydrophobic
N6AOCYS- 1592.89157H-Bond
(Ligand Donor)
O1ANE2HIS- 1622.96170.79H-Bond
(Protein Donor)
DuArDuArHIS- 1623.940Aromatic Face/Face
N6AOD1ASN- 1633126.05H-Bond
(Ligand Donor)
C6CG2VAL- 1654.120Hydrophobic
C9ACG1VAL- 1654.230Hydrophobic
C2'CG1VAL- 1654.160Hydrophobic
N7AND2ASN- 1663.13167.02H-Bond
(Protein Donor)
O4NZLYS- 1683.46157.06H-Bond
(Protein Donor)
C2'CD1LEU- 1693.760Hydrophobic
O1PNZLYS- 1712.85155.75H-Bond
(Protein Donor)
O1PNZLYS- 1712.850Ionic
(Protein Cationic)
DuArDuArPHE- 1743.790Aromatic Face/Face
C2BCE1PHE- 17440Hydrophobic
O2BNEARG- 1822.83155.41H-Bond
(Protein Donor)
C4BCZ2TRP- 1834.420Hydrophobic
C1BCZ2TRP- 1834.040Hydrophobic
N3ANE1TRP- 1832.97165.5H-Bond
(Protein Donor)
O4'OHOH- 3122.67138.76H-Bond
(Ligand Donor)