8ONM

Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A complexed with D-glutamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

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

Probing of the structural and catalytic roles of the residues in the active site of transaminase from Aminobacterium colombiense

Shilova, S.A.Khrenova, M.G.Matyuta, I.O.Nikolaeva, A.Y.Klyachko, N.L.Minyaev, M.E.Boyko, K.M.Popov, V.O.Bezsudnova, E.Y.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminotransferase class IV
A, B
277Aminobacterium colombienseMutation(s): 1 
Gene Names: Amico_1844
UniProt
Find proteins for D5EHC5 (Aminobacterium colombiense (strain DSM 12261 / ALA-1))
Explore D5EHC5 
Go to UniProtKB:  D5EHC5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD5EHC5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PW0 (Subject of Investigation/LOI)
Query on PW0

Download Ideal Coordinates CCD File 
G [auth B](~{Z})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pent-2-enedioic acid
C13 H17 N2 O9 P
AQYBBWUPMNWMHD-UHFFFAOYSA-N
PMP (Subject of Investigation/LOI)
Query on PMP

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B],
I [auth B],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
L [auth B],
M [auth B]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.4α = 90
b = 89.435β = 90
c = 101.311γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
CrysalisProdata reduction
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Russian Science FoundationRussian Federation19-14-00164

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-10
    Type: Initial release