2WEF | pdb_00002wef

Human 3'(2'), 5'-bisphosphate nucleotidase 1 (BPNT1) in complex with AMP, PO4 and Magnesium

• PDB DOI: https://doi.org/10.2210/pdb2WEF/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-03-30 Released: 2009-04-14 
• Deposition Author(s): Moche, M., Schutz, P., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Schueler, H., Siponen, M.I., Thorsell, A.G., Tresaugues, L., Van Der Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.189 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Starting Model: experimental

Literature

Human 3'(2'), 5'-Bisphosphate Nucleotidase 1 (Bpnt1) in Complex with AMP, Po4 and Magnesium

Moche, M., Schutz, P., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Schueler, H., Siponen, M.I., Thorsell, A.G., Tresaugues, L., Van Den Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 34.48 kDa 
• Atom Count: 2,612 
• Modeled Residue Count: 303 
• Deposited Residue Count: 311 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3'(2')\, 5'-BISPHOSPHATE NUCLEOTIDASE 1	A	311	Homo sapiens	Mutation(s): 0  EC: 3.1.3.7 (PDB Primary Data), 3.1.3.57 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O95861 (Homo sapiens) Explore O95861  Go to UniProtKB:  O95861
PHAROS:  O95861 GTEx:  ENSG00000162813

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	F [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
PO4	E [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	B [auth A], C [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.189 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.98	α = 90
b = 67.664	β = 90
c = 100.394	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-14 
Deposition Author(s): Moche, M., Schutz, P., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Dahlgren, L.G., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Karlberg, T., Kotenyova, T., Nilsson, M.E., Nyman, T., Persson, C., Sagemark, J., Schueler, H., Siponen, M.I., Thorsell, A.G., Tresaugues, L., Van Der Berg, S., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-04-14
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Derived calculations, Other, Structure summary, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description