4ZQB

Crystal structure of NADP-dependent dehydrogenase from Rhodobactersphaeroides in complex with NADP and sulfate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of NADP-dependent dehydrogenase from Rhodobactersphaeroides in complex with NADP and sulfate

Kowiel, M.Gasiorowska, O.A.Shabalin, I.G.Handing, K.B.Porebski, P.J.Bonanno, J.Almo, S.C.Minor, W.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NADP-dependent dehydrogenaseA, B316Cereibacter sphaeroides 2.4.1Mutation(s): 0 
Gene Names: RSP_3442
EC: 1.1.1.79 (PDB Primary Data), 1.1.1.81 (PDB Primary Data)
UniProt
Find proteins for Q3IWN8 (Cereibacter sphaeroides (strain ATCC 17023 / DSM 158 / JCM 6121 / CCUG 31486 / LMG 2827 / NBRC 12203 / NCIMB 8253 / ATH 2.4.1.))
Explore Q3IWN8 
Go to UniProtKB:  Q3IWN8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3IWN8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
PGE
Query on PGE

Download Ideal Coordinates CCD File 
E [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

Download Ideal Coordinates CCD File 
K [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
H [auth B],
I [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
J [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.489α = 90
b = 71.489β = 90
c = 244.364γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
Cootmodel building
REFMACrefinement
HKL-3000phasing
MOLREPphasing
HKL-3000data scaling
HKL-3000data reduction
BLU-MAXdata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-05-20
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description, Source and taxonomy, Structure summary
  • Version 1.2: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.3: 2022-04-13
    Changes: Database references, Structure summary