8SAB

Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes, PLP adduct with Alanine (C2 form)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Crystal Structure of Cystathionine beta lyase from Klebsiella aerogenes, PLP adduct with Alanine (C2 form)

Liu, L.Lovell, S.Battaile, K.P.Cooper, A.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cystathionine beta-lyase
A, B
403Klebsiella aerogenes KCTC 2190Mutation(s): 2 
Gene Names: EAE_03480
EC: 4.4.1.8
UniProt
Find proteins for A0A0H3FMF8 (Klebsiella aerogenes (strain ATCC 13048 / DSM 30053 / CCUG 1429 / JCM 1235 / KCTC 2190 / NBRC 13534 / NCIMB 10102 / NCTC 10006 / CDC 819-56))
Explore A0A0H3FMF8 
Go to UniProtKB:  A0A0H3FMF8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H3FMF8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PP3 (Subject of Investigation/LOI)
Query on PP3

Download Ideal Coordinates CCD File 
D [auth A],
L [auth B]
ALANYL-PYRIDOXAL-5'-PHOSPHATE
C11 H17 N2 O7 P
WACJCHFWJNNBPR-ZETCQYMHSA-N
PLP (Subject of Investigation/LOI)
Query on PLP

Download Ideal Coordinates CCD File 
E [auth A],
M [auth B]
PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
LYS
Query on LYS

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O
TRS
Query on TRS

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

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
N [auth B]
O [auth B]
F [auth A],
G [auth A],
H [auth A],
N [auth B],
O [auth B],
P [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
Q [auth B]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.325α = 90
b = 130.522β = 103.96
c = 82.366γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93022C00036
National Institutes of Health/Office of the DirectorUnited StatesOD030394

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-12
    Type: Initial release