8BXX

Crystal structure of formate dehydrogenase FDH2 enzyme from Granulicella mallensis MP5ACTX8 in complex with NAD and azide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 6T8J


Literature

From the amelioration of a NADP+-dependent formate dehydrogenase to the discovery of a new enzyme: round trip from theory to practice

Rubini, R.Robescu, M.S.Tavanti, M.Beneventi, E.Lonigro, C.Niero, M.Zito, F.Filippini, F.Cendron, L.Bergantino, E.

(2020) ChemCatChem 


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenaseA [auth AA],
B [auth BB],
C [auth CC],
D [auth DD]
386Granulicella mallensis MP5ACTX8Mutation(s): 0 
Gene Names: AciX8_0868
EC: 1.17.1.9
UniProt
Find proteins for G8NTI5 (Granulicella mallensis (strain ATCC BAA-1857 / DSM 23137 / MP5ACTX8))
Explore G8NTI5 
Go to UniProtKB:  G8NTI5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG8NTI5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD (Subject of Investigation/LOI)
Query on NAD

Download Ideal Coordinates CCD File 
E [auth AA],
H [auth BB],
K [auth CC],
N [auth DD]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth AA],
J [auth BB],
M [auth CC],
P [auth DD]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
AZI (Subject of Investigation/LOI)
Query on AZI

Download Ideal Coordinates CCD File 
F [auth AA],
I [auth BB],
L [auth CC],
O [auth DD]
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.97 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.188 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.066α = 90
b = 128.81β = 100.4
c = 85.664γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Italian Ministry of EducationItaly--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2024-06-19
    Changes: Data collection