8OQ2

Binding of NADP to a formate dehydrogenase from Starkeya novella.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.237 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 7QZ1


Literature

Binding of NADP to a formate dehydrogenase from Starkeya novella.

Partipilo, M.Whittaker, J.J.Pontillo, N.Coenradij, J.Herrmann, A.Guskov, A.Slotboom, D.J.

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
381Ancylobacter novellusMutation(s): 4 
Gene Names: Snov_3272
EC: 1.17.1.9
UniProt
Find proteins for D7A8L2 (Ancylobacter novellus (strain ATCC 8093 / DSM 506 / JCM 20403 / CCM 1077 / IAM 12100 / NBRC 12443 / NCIMB 10456))
Explore D7A8L2 
Go to UniProtKB:  D7A8L2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7A8L2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
G [auth A]
H [auth B]
P [auth C]
X [auth D]
Y [auth E]
G [auth A],
H [auth B],
P [auth C],
X [auth D],
Y [auth E],
Z [auth F]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
AZI
Query on AZI

Download Ideal Coordinates CCD File 
I [auth B]
J [auth B]
K [auth B]
L [auth B]
M [auth B]
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
Q [auth C],
R [auth C],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C]
AZIDE ION
N3
IVRMZWNICZWHMI-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.237 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.265α = 90
b = 132.265β = 90
c = 302.952γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Netherlands Organisation for Scientific Research (NWO)Netherlands024.003.019

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release