Brand  (β version)

PDB ID: 4MWO

Hetero Atom Contents

  The number of atoms exceeds 100,000.
  So, it can not be displayed here.

Select unit:

Color scheme of protein:

Code Name Style Show Link
2E2 1-{3,5-O-[(4-carboxyphenyl)(phosphono)methylidene]-2-deoxy-beta-D-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1h,3h)-dione PoSSuM
GOL Glycerol PoSSuM
K Potassium ion PoSSuM
PO4 Phosphate ion PoSSuM

Select hetatm:   

Select hetatm:   

Select chain:  

Data format:   

Non-standard Residues
Code Name Show
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 4MWO   PDBj   RCSB PDB   PDBe
Header : HYDROLASE/HYDROLASE INHIBITOR
Title : Crystal structure of human mitochondrial 5'(3')-deoxyribonucleotidase in complex with the inhibitor CPB-T
Release Data : 2014-09-10
Compound :
mol_id molecule chains synonym
1 5'(3')-deoxyribonucleotidase, mitochondrial A 5',3'-nucleotidase, mitochondrial, Deoxy-5'-nucleotidase 2, dNT-2
ec: 3.1.3.-
fragment: UNP residues 32-227
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:469008)
gene: DNT1, DNT2, NT5C, NT5M, UMPH2
expression_system_strain: BL21(DE3)
expression_system_vector_type: plasmid
expression_system_plasmid: pMCSG7
Authors : Pachl, P., Rezacova, P., Brynda, J.
Keywords : 5'-nucleotidase, protein conformation, dephosphorylation, phosphorylation, HAD-like, mitochondia, HYDROLASE-HYDROLASE INHIBITOR complex
Exp. method : X-RAY DIFFRACTION ( 1.670 Å )
Citation :

Conformationally constrained nucleoside phosphonic acids - potent inhibitors of human mitochondrial and cytosolic 5'(3')-nucleotidases.

Simak, O.,Pachl, P.,Fabry, M.  et al.
(2014)  Org.Biomol.Chem.  12 : 7971 - 7982

PubMed: 25178098
DOI: 10.1039/c4ob01332h

Reaction

Chain : A
UniProt : Q9NPB1 (NT5M_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
dTMP + H2O = thymidine + phosphate - PubMed:10899995, PubMed:16004879
-
dUMP + H2O = 2'-deoxyuridine + phosphate - PubMed:10899995, PubMed:16004879
-
UMP + H2O = uridine + phosphate - PubMed:10899995, PubMed:16004879
-
thymidine 3'-phosphate + H2O = thymidine + phosphate - PubMed:10899995, PubMed:16004879
-
uridine 2'-phosphate + H2O = uridine + phosphate - PubMed:10899995, PubMed:16004879
-
3'-UMP + H2O = uridine + phosphate - PubMed:10899995
-
dGMP + H2O = 2'-deoxyguanosine + phosphate - PubMed:16004879
-
Cofactor: Evidence: Note:
Mg(2+) ECO:0000269 | PubMed:16004879
-