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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:

2a4x

1.400 Å

X-ray

2005-06-30

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Mitomycin-binding protein
ID:O05205_STRLA
AC:O05205
Organism:Streptomyces lavendulae
Reign:Bacteria
TaxID:1914
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
A59 %
B41 %


Ligand binding site composition:

B-Factor:17.581
Number of residues:32
Including
Standard Amino Acids: 32
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.855570.375

% Hydrophobic% Polar
57.4042.60
According to VolSite

Ligand :
2a4x_1 Structure
HET Code: BLM
Formula: C55H86N17O21S3
Molecular weight: 1417.568 g/mol
DrugBank ID: DB00290
Buried Surface Area:43.57 %
Polar Surface area: 692.33 Å2
Number of
H-Bond Acceptors: 28
H-Bond Donors: 21
Rings: 6
Aromatic rings: 4
Anionic atoms: 0
Cationic atoms: 1
Rule of Five Violation: 3
Rotatable Bonds: 36

Mass center Coordinates

XYZ
10.0027.003127.6738


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
C54CBALA- 744.220Hydrophobic
NLOE2GLU- 783.660Ionic
(Ligand Cationic)
NLOE1GLU- 783.590Ionic
(Ligand Cationic)
S43CBTRP- 1084.090Hydrophobic
O40NE2GLN- 1102.99163.78H-Bond
(Protein Donor)
C55CD1ILE- 1143.770Hydrophobic
C54CD1ILE- 1144.040Hydrophobic
S53CD1ILE- 1144.450Hydrophobic
C54CG1VAL- 1223.470Hydrophobic
C52CD1TYR- 2604.330Hydrophobic
C55CBTYR- 2604.370Hydrophobic