8AIE

Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense complexed with D-cycloserine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

3D Structure of D-Аmino Acid Тransaminase from Aminobacterium colombiense in Complex with D-Cycloserine

Shilova, S.A.Matyuta, I.O.Bezsudnova, E.Y.Minyaev, M.E.Nikolaeva, A.Y.Popov, V.O.Boyko, K.M.

(2023) Crystallogr Rep 68: 931-937


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Aminotransferase class IV
A, B
277Aminobacterium colombienseMutation(s): 0 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
M7L (Subject of Investigation/LOI)
Query on M7L

Download Ideal Coordinates CCD File 
E [auth B]3-azanyloxy-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]propanoic acid
C11 H16 N3 O8 P
ICHYGZXBYNDCFX-NTEUORMPSA-N
LCS (Subject of Investigation/LOI)
Query on LCS

Download Ideal Coordinates CCD File 
C [auth A][5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate
C11 H14 N3 O7 P
KFCQHWOGBVCKHR-UKTHLTGXSA-N
PMP (Subject of Investigation/LOI)
Query on PMP

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE
C8 H13 N2 O5 P
ZMJGSOSNSPKHNH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.968α = 90
b = 90.028β = 90
c = 100.29γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
CrysalisProdata reduction
REFMACphasing

Structure Validation

View Full Validation Report



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: 2022-11-16
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-03-06
    Changes: Database references