9C35 | pdb_00009c35

Proline utilization A with the covalent acyl-enzyme intermediate in the aldehyde dehydrogenase active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.249 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

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

Visualization of transient states and molecular motions in the catalytic cycle of the proline catabolic bifunctional enzyme Proline Utilization A from kinetic crystallography and molecular dynamics simulations

Buckley, D.P.Gamage, T.Campbell, A.C.Becker, D.F.Tanner, J.J.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional protein PutA
A, B
1,235Sinorhizobium meliloti SM11Mutation(s): 1 
Gene Names: putASM11_chr0102
EC: 1.5.5.2 (PDB Primary Data), 1.2.1.88 (PDB Primary Data)
UniProt
Find proteins for F7X6I3 (Sinorhizobium meliloti (strain SM11))
Explore F7X6I3 
Go to UniProtKB:  F7X6I3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF7X6I3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FDA (Subject of Investigation/LOI)
Query on FDA

Download Ideal Coordinates CCD File 
I [auth A],
O [auth B]
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE
C27 H35 N9 O15 P2
YPZRHBJKEMOYQH-UYBVJOGSSA-N
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
C [auth A],
K [auth B]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
E [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
A1AUG (Subject of Investigation/LOI)
Query on A1AUG

Download Ideal Coordinates CCD File 
G [auth A]5-oxo-L-norvaline
C5 H9 N O3
KABXUUFDPUOJMW-BYPYZUCNSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
M [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
J [auth A],
L [auth B],
P [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
H [auth A],
N [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.249 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.779α = 90
b = 103.119β = 106.51
c = 127.918γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM065546

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release