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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:

4l2z

2.490 Å

X-ray

2013-06-05

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:S-adenosylmethionine synthase
ID:METK_SULSO
AC:Q980S9
Organism:Sulfolobus solfataricus
Reign:Archaea
TaxID:273057
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A47 %
B53 %


Ligand binding site composition:

B-Factor:31.034
Number of residues:45
Including
Standard Amino Acids: 41
Non Standard Amino Acids: 2
Water Molecules: 2
Cofactors:
Metals: MG MG

Cavity properties

LigandabilityVolume (Å3)
0.213401.625

% Hydrophobic% Polar
46.2253.78
According to VolSite

Ligand :
4l2z_1 Structure
HET Code: S7M
Formula: C16H25N6O5S
Molecular weight: 413.472 g/mol
DrugBank ID: -
Buried Surface Area:70.94 %
Polar Surface area: 189.77 Å2
Number of
H-Bond Acceptors: 9
H-Bond Donors: 4
Rings: 3
Aromatic rings: 2
Anionic atoms: 1
Cationic atoms: 2
Rule of Five Violation: 1
Rotatable Bonds: 8

Mass center Coordinates

XYZ
29.62951.05596.69843


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
O8NE2HIS- 583.12157.76H-Bond
(Protein Donor)
O7ND2ASN- 602.96160.96H-Bond
(Protein Donor)
C28CD2LEU- 1453.970Hydrophobic
C1CD1LEU- 1453.490Hydrophobic
O8ND2ASN- 1592.99165.45H-Bond
(Protein Donor)
C28CBASP- 1603.70Hydrophobic
O26OD1ASP- 1992.92135.49H-Bond
(Ligand Donor)
O26OD2ASP- 1993.45150.01H-Bond
(Ligand Donor)
C14CBALA- 2164.360Hydrophobic
DuArDuArTYR- 2703.950Aromatic Face/Face
C14CZTYR- 2704.440Hydrophobic
C13CBSER- 2774.130Hydrophobic
S2CBASP- 2824.170Hydrophobic
C12CBASP- 2824.140Hydrophobic
N9OD1ASP- 2822.77147.37H-Bond
(Ligand Donor)
O27OD2ASP- 2822.74167.8H-Bond
(Ligand Donor)
N9OD1ASP- 2822.770Ionic
(Ligand Cationic)
C28CD1ILE- 3493.780Hydrophobic
N25OHOH- 7173162.24H-Bond
(Ligand Donor)