Bd2924 apo-form

Experimental Data Snapshot

  • 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 1.3 of the entry. See complete history


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: https://doi.org/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.

  • Organizational Affiliation

    BSC-CNS Barcelona Supercomputing Center, Barcelona, Spain.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable acyl-CoA dehydrogenaseA [auth X],
B [auth A]
505Bdellovibrio bacteriovorus HD100Mutation(s): 0 
Gene Names: Bd2924
EC: 1.3.99
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
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FAD

Download Ideal Coordinates CCD File 
C [auth X],
D [auth A]
C27 H33 N9 O15 P2
Experimental Data & Validation

Experimental Data

  • 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
XDSdata reduction
Aimlessdata scaling
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
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references, Refinement description