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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:

5prc

2.350 Å

X-ray

1997-08-01

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Reaction center protein L chain
ID:RCEL_BLAVI
AC:P06009
Organism:Blastochloris viridis
Reign:Bacteria
TaxID:1079
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
L91 %
M5 %
H5 %


Ligand binding site composition:

B-Factor:26.322
Number of residues:26
Including
Standard Amino Acids: 22
Non Standard Amino Acids: 2
Water Molecules: 2
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
1.347320.625

% Hydrophobic% Polar
77.8922.11
According to VolSite

Ligand :
5prc_1 Structure
HET Code: ATZ
Formula: C8H14ClN5
Molecular weight: 215.683 g/mol
DrugBank ID: DB07392
Buried Surface Area:62.2 %
Polar Surface area: 62.73 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 2
Rings: 1
Aromatic rings: 1
Anionic atoms: 0
Cationic atoms: 0
Rule of Five Violation: 0
Rotatable Bonds: 4

Mass center Coordinates

XYZ
131.97469.517-3.66871


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
CL2CBLEU- 1893.840Hydrophobic
C9CD1LEU- 1894.350Hydrophobic
CL2CBHIS- 1904.280Hydrophobic
C12CD2LEU- 1933.970Hydrophobic
C13CBGLU- 2123.90Hydrophobic
CL2CE2PHE- 2163.810Hydrophobic
C8CGPHE- 2164.410Hydrophobic
C9CD1PHE- 2163.520Hydrophobic
DuArDuArPHE- 2163.930Aromatic Face/Face
C9CG2VAL- 2203.730Hydrophobic
N7OTYR- 2223.04136.77H-Bond
(Ligand Donor)
N11OGSER- 2232.93163.23H-Bond
(Ligand Donor)
N5NILE- 2242.9153.91H-Bond
(Protein Donor)
C10CG2ILE- 2244.430Hydrophobic
C13CBALA- 2264.470Hydrophobic
CL2CG1ILE- 2293.760Hydrophobic