6NFE

Crystal Structure of Ribose-phosphate Pyrophosphokinase from Legionella pneumophila with bound AMP, ADP, and Ribose-5-Phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.152 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history


Literature

Crystal Structure of Ribose-phosphate Pyrophosphokinase from Legionella pneumophila with bound AMP, ADP, and Ribose-5-Phosphate

Bolejack, M.J.Abendroth, J.Lorimer, D.D.Horanyi, P.S.Edwards, T.E.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribose-phosphate pyrophosphokinase
A, B
323Legionella pneumophilaMutation(s): 0 
Gene Names: prsAprsC3927_02005NCTC12024_00599
EC: 2.7.6.1
UniProt
Find proteins for Q5ZY30 (Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513))
Explore Q5ZY30 
Go to UniProtKB:  Q5ZY30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5ZY30
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
N [auth A],
P [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
AMP
Query on AMP

Download Ideal Coordinates CCD File 
H [auth A],
J [auth A]
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
HSX
Query on HSX

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E [auth A],
T [auth B]
5-O-phosphono-alpha-D-ribofuranose
C5 H11 O8 P
KTVPXOYAKDPRHY-AIHAYLRMSA-N
EDO
Query on EDO

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C [auth A]
F [auth A]
I [auth A]
K [auth A]
L [auth A]
C [auth A],
F [auth A],
I [auth A],
K [auth A],
L [auth A],
M [auth A],
O [auth A],
Q [auth B],
R [auth B],
S [auth B],
V [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
EOH
Query on EOH

Download Ideal Coordinates CCD File 
D [auth A],
G [auth A],
U [auth B]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109α = 90
b = 109β = 90
c = 97.3γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
MoRDaphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations
  • Version 2.1: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary