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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:

4zm3

2.270 Å

X-ray

2015-05-02

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Aminotransferase
ID:A8R0K5_9ACTN
AC:A8R0K5
Organism:Streptomyces pactum
Reign:Bacteria
TaxID:68249
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C8 %
D92 %


Ligand binding site composition:

B-Factor:25.388
Number of residues:28
Including
Standard Amino Acids: 26
Non Standard Amino Acids: 0
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.749945.000

% Hydrophobic% Polar
38.9361.07
According to VolSite

Ligand :
4zm3_4 Structure
HET Code: PLP
Formula: C8H8NO6P
Molecular weight: 245.126 g/mol
DrugBank ID: DB00114
Buried Surface Area:59.01 %
Polar Surface area: 132.42 Å2
Number of
H-Bond Acceptors: 7
H-Bond Donors: 1
Rings: 1
Aromatic rings: 1
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
12.92810.15787555.3999


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
O3PNGLY- 1202.79161.21H-Bond
(Protein Donor)
O2PNTHR- 1212.83152.87H-Bond
(Protein Donor)
O2POG1THR- 1212.68153.57H-Bond
(Protein Donor)
C5ACE2TYR- 1474.320Hydrophobic
C2ACGGLU- 2153.780Hydrophobic
N1OD1ASP- 2483.27123.08H-Bond
(Ligand Donor)
N1OD2ASP- 2482.54172.96H-Bond
(Ligand Donor)
C2ACBVAL- 2504.170Hydrophobic
C3CG1VAL- 2503.520Hydrophobic
C2ACD1ILE- 25140Hydrophobic
C3CD1ILE- 2514.40Hydrophobic