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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:

3s6a

2.200 Å

X-ray

2011-05-25

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Adenosine monophosphate-protein transferase NmFic
ID:NMFIC_NEIMB
AC:Q7DDR9
Organism:Neisseria meningitidis serogroup B
Reign:Bacteria
TaxID:122586
EC Number:2.7.7.n1


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:32.639
Number of residues:36
Including
Standard Amino Acids: 34
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.343496.125

% Hydrophobic% Polar
51.7048.30
According to VolSite

Ligand :
3s6a_1 Structure
HET Code: ANP
Formula: C10H13N6O12P3
Molecular weight: 502.164 g/mol
DrugBank ID: -
Buried Surface Area:64.72 %
Polar Surface area: 322.68 Å2
Number of
H-Bond Acceptors: 16
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 4
Cationic atoms: 0
Rule of Five Violation: 2
Rotatable Bonds: 8

Mass center Coordinates

XYZ
-25.058767.6706-5.162


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
O2ANZLYS- 672.65170.28H-Bond
(Protein Donor)
O3ANZLYS- 673.42120.39H-Bond
(Protein Donor)
O2ANZLYS- 672.650Ionic
(Protein Cationic)
N3ND2ASN- 1042.84173.89H-Bond
(Protein Donor)
O2ANE2HIS- 1072.96159.36H-Bond
(Protein Donor)
O1ANASN- 1132.86157.88H-Bond
(Protein Donor)
O1AND2ASN- 1132.83158.54H-Bond
(Protein Donor)
O2BNGLY- 1143.49147.56H-Bond
(Protein Donor)
O5'NGLY- 1143.15126.5H-Bond
(Protein Donor)
O3'NH1ARG- 1182.97154.49H-Bond
(Protein Donor)
C2'CE2TYR- 1434.350Hydrophobic
O2'OHTYR- 1433.12143.77H-Bond
(Ligand Donor)
C3'CD2LEU- 1444.180Hydrophobic
C2'CGMET- 1473.90Hydrophobic
C1'CBMET- 1474.350Hydrophobic
C5'CGGLU- 1864.130Hydrophobic
O3'OE2GLU- 1862.83160.4H-Bond
(Ligand Donor)
O3'OE1GLU- 1863133.79H-Bond
(Ligand Donor)