7SU8

DIHYDRONEOPTERIN ALDOLASE (DHNA) FROM YERSINIA PESTIS with alkylated Cys50 CO-CRYSTALLIZED with 7,8-dihydroneopterin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.211 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

DIHYDRONEOPTERIN ALDOLASE (DHNA) FROM YERSINIA PESTIS with alkylated Cys50 CO-CRYSTALLIZED with 7,8-dihydroneopterin

Bourne, C.R.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
7,8-dihydroneopterin aldolase
A, B
143Yersinia pestisMutation(s): 0 
Gene Names: y3531
EC: 4.1.2.25
UniProt
Find proteins for A0A5P8YJX5 (Yersinia pestis)
Explore A0A5P8YJX5 
Go to UniProtKB:  A0A5P8YJX5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A5P8YJX5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PH2 (Subject of Investigation/LOI)
Query on PH2

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
2-AMINO-6-HYDROXYMETHYL-7,8-DIHYDRO-3H-PTERIDIN-4-ONE
C7 H9 N5 O2
CQQNNQTXUGLUEV-UHFFFAOYSA-N
NEN (Subject of Investigation/LOI)
Query on NEN

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
1-ETHYL-PYRROLIDINE-2,5-DIONE
C6 H9 N O2
GHAZCVNUKKZTLG-UHFFFAOYSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
H [auth B]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD
Query on MPD

Download Ideal Coordinates CCD File 
E [auth B],
I [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.211 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.604α = 90
b = 72.604β = 90
c = 105.96γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2022-12-28 
  • Deposition Author(s): Bourne, C.R.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103447

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-10-30
    Changes: Structure summary