6SD8

Bd2924 apo-form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Target highlights in CASP13: Experimental target structures through the eyes of their authors.

Lepore, R.Kryshtafovych, A.Alahuhta, M.Veraszto, H.A.Bomble, Y.J.Bufton, J.C.Bullock, A.N.Caba, C.Cao, H.Davies, O.R.Desfosses, A.Dunne, M.Fidelis, K.Goulding, C.W.Gurusaran, M.Gutsche, I.Harding, C.J.Hartmann, M.D.Hayes, C.S.Joachimiak, A.Leiman, P.G.Loppnau, P.Lovering, A.L.Lunin, V.V.Michalska, K.Mir-Sanchis, I.Mitra, A.K.Moult, J.Phillips Jr., G.N.Pinkas, D.M.Rice, P.A.Tong, Y.Topf, M.Walton, J.D.Schwede, T.

(2019) Proteins 87: 1037-1057

  • DOI: 10.1002/prot.25805
  • Primary Citation of Related Structures:  
    6CVZ, 6SD8, 6SDA

  • PubMed Abstract: 
  • The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment ...

    The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment.


    Organizational Affiliation

    SIB Swiss Institute of Bioinformatics, Biozentrum University of Basel, Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable acyl-CoA dehydrogenaseB [auth A],
A [auth X]
505Bdellovibrio bacteriovorus HD100Mutation(s): 0 
Gene Names: Bd2924
EC: 1.3.99
UniProt
Find proteins for Q6MJ59 (Bdellovibrio bacteriovorus (strain ATCC 15356 / DSM 50701 / NCIMB 9529 / HD100))
Explore Q6MJ59 
Go to UniProtKB:  Q6MJ59
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6MJ59
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth X],
D [auth A]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.174 
  • R-Value Observed: 0.175 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 137.75α = 90
b = 113.012β = 120.84
c = 89.044γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdomstudentship

Revision History  (Full details and data files)

  • Version 1.0: 2019-09-11
    Type: Initial release
  • Version 1.1: 2019-11-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Database references