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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:

1mc1

2.160 Å

X-ray

2002-08-04

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Carboxyethyl-arginine beta-lactam-synthase
ID:BLS_STRCL
AC:P0DJQ7
Organism:Streptomyces clavuligerus
Reign:Bacteria
TaxID:1901
EC Number:6.3.3.4


Chains:

Chain Name:Percentage of Residues
within binding site
A100 %


Ligand binding site composition:

B-Factor:29.806
Number of residues:29
Including
Standard Amino Acids: 25
Non Standard Amino Acids: 3
Water Molecules: 1
Cofactors: AMP
Metals: MG MG

Cavity properties

LigandabilityVolume (Å3)
0.662502.875

% Hydrophobic% Polar
50.3449.66
According to VolSite

Ligand :
1mc1_1 Structure
HET Code: PCX
Formula: C9H16N4O3
Molecular weight: 228.248 g/mol
DrugBank ID: DB02475
Buried Surface Area:67.82 %
Polar Surface area: 124.07 Å2
Number of
H-Bond Acceptors: 5
H-Bond Donors: 3
Rings: 1
Aromatic rings: 0
Anionic atoms: 1
Cationic atoms: 1
Rule of Five Violation: 0
Rotatable Bonds: 7

Mass center Coordinates

XYZ
-7.309288.623360.5947


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
C5CD1ILE- 3234.180Hydrophobic
C2CD1TYR- 3264.20Hydrophobic
C4CE1TYR- 3263.620Hydrophobic
C2CZTYR- 3483.640Hydrophobic
O2NGLY- 3493.05162.68H-Bond
(Protein Donor)
C5CD1ILE- 3523.760Hydrophobic
N3OE2GLU- 3822.91140.7H-Bond
(Ligand Donor)
O4NZLYS- 4432.99135.52H-Bond
(Protein Donor)