6R62

Crystal structure of a class II pyruvate aldolase from Sphingomonas wittichii RW1 in complex with hydroxypyruvate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

CH-Pi Interactions Promote the Conversion of Hydroxypyruvate in a Class II Pyruvate Aldolase

Marsden, S.R.Mestrom, L.Bento, I.Hagedoorn, P.L.McMillan, D.G.G.Hanefeld, U.

(2019) Adv Synth Catal 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HpcH/HpaI aldolase252Rhizorhabdus wittichii RW1Mutation(s): 0 
Gene Names: Swit_5035
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3PY
Query on 3PY

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
3-HYDROXYPYRUVIC ACID
C3 H4 O4
HHDDCCUIIUWNGJ-UHFFFAOYSA-N
BR
Query on BR

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F [auth A],
G [auth A]
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
ACT
Query on ACT

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D [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
K
Query on K

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H [auth A],
I [auth A]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG
Query on MG

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E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

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J [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 42 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.569α = 90
b = 116.569β = 90
c = 116.569γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2024-05-15
    Changes: Data collection, Database references, Derived calculations