3N7U

NAD-dependent formate dehydrogenase from higher-plant Arabidopsis thaliana in complex with NAD and azide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structures of the apo and holo forms of NAD-dependent formate dehydrogenase from the higher-plant Arabidopsis Thaliana

Shabalin, I.G.Polyakov, K.M.Skirgello, O.E.Tishkov, V.I.Popov, V.O.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Formate dehydrogenase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
351Arabidopsis thalianaMutation(s): 0 
Gene Names: At5g14780FDHFDH1T9L3_80
EC: 1.2.1.2
UniProt
Find proteins for Q9S7E4 (Arabidopsis thaliana)
Explore Q9S7E4 
Go to UniProtKB:  Q9S7E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9S7E4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
BB [auth J]
DB [auth K]
FA [auth E]
IA [auth F]
JB [auth L]
BB [auth J],
DB [auth K],
FA [auth E],
IA [auth F],
JB [auth L],
M [auth A],
MA [auth G],
P [auth B],
QA [auth H],
T [auth C],
VA [auth I],
Y [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
FB [auth K]
KA [auth F]
O [auth A]
OA [auth G]
AA [auth D],
FB [auth K],
KA [auth F],
O [auth A],
OA [auth G],
R [auth B],
SA [auth H],
V [auth C],
XA [auth I]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AB [auth I]
BA [auth D]
CA [auth D]
DA [auth D]
EA [auth D]
AB [auth I],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
GB [auth K],
HA [auth E],
HB [auth K],
IB [auth K],
LA [auth F],
LB [auth L],
PA [auth G],
S [auth B],
TA [auth H],
UA [auth H],
W [auth C],
X [auth C],
YA [auth I],
ZA [auth I]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
AZI
Query on AZI

Download Ideal Coordinates CCD File 
CB [auth J]
EB [auth K]
GA [auth E]
JA [auth F]
KB [auth L]
CB [auth J],
EB [auth K],
GA [auth E],
JA [auth F],
KB [auth L],
N [auth A],
NA [auth G],
Q [auth B],
RA [auth H],
U [auth C],
WA [auth I],
Z [auth D]
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 229.62α = 90
b = 217.68β = 92.62
c = 139.11γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
AUTOMARdata collection
XDSdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations