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PDBsum entry 3mk0

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protein ligands metals links
Hydrolase PDB id
3mk0
Jmol
Contents
Protein chain
481 a.a. *
Ligands
NAG-NAG ×2
NPO ×2
PO4
ACT
Metals
_ZN ×2
_MG
_CA
Waters ×527
* Residue conservation analysis
PDB id:
3mk0
Name: Hydrolase
Title: Refinement of placental alkaline phosphatase complexed with nitrophenyl
Structure: Alkaline phosphatase, placental type. Chain: a. Synonym: placental alkaline phosphatase 1, plap-1, alkaline phosphatase regan isozyme. Ec: 3.1.3.1
Source: Homo sapiens. Human. Organism_taxid: 9606
Resolution:
1.90Å     R-factor:   0.137     R-free:   0.190
Authors: B.Stec,A.Cheltsov,J.L.Millan
Key ref: B.Stec et al. (2010). Refined structures of placental alkaline phosphatase show a consistent pattern of interactions at the peripheral site. Acta Crystallogr Sect F Struct Biol Cryst Commun, 66, 866-870. PubMed id: 20693656
Date:
13-Apr-10     Release date:   19-Jan-11    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P05187  (PPB1_HUMAN) -  Alkaline phosphatase, placental type
Seq:
Struc:
 
Seq:
Struc:
535 a.a.
481 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.3.1  - Alkaline phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: A phosphate monoester + H2O = an alcohol + phosphate
phosphate monoester
+ H(2)O
= alcohol
+
phosphate
Bound ligand (Het Group name = PO4)
corresponds exactly
      Cofactor: Magnesium; Zinc
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cell surface   5 terms 
  Biological process     metabolic process   2 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
Acta Crystallogr Sect F Struct Biol Cryst Commun 66:866-870 (2010)
PubMed id: 20693656  
 
 
Refined structures of placental alkaline phosphatase show a consistent pattern of interactions at the peripheral site.
B.Stec, A.Cheltsov, J.L.Millán.
 
  ABSTRACT  
 
In order to gain deeper insights into the functional sites of human placental alkaline phosphatase, the structures of the enzyme with the putative regulators L-Phe, pNPP and 5'-AMP [Llinas et al. (2005), J. Mol. Biol. 350, 441-451] were re-refined. Significant variations in ligand positioning and identity were found compared with the previous report. The multiple corrections to the model improved the phases and the electron-density maps, allowing the modeling of omitted side chains and multiple disordered residues. These improvements led to a change in the position of L-Phe at the peripheral binding site, which appeared to be reversed. The structure with pNPP contained only p-nitrophenol in three distinct sites, while the structure with 5'-AMP contained the p-nitrophenyl group in two of the sites instead of 5'-AMP. Comparison of the re-refined models shows a consistent pattern of interactions at the peripheral site.