1X9J

Structure of butyrate kinase 2 reveals both open- and citrate-induced closed conformations: implications for substrate-induced fit conformational changes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.261 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of butyrate kinase 2 reveals both open and closed conformations of the two domains: implications for substrate-induced changes

Diao, J.S.Bhattacharyya, S.Ma, Y.L.D.Sanders, D.A.Hasson, M.S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable butyrate kinase 2
A, B, C, D, E
A, B, C, D, E, F, G, H
375Thermotoga maritimaMutation(s): 0 
Gene Names: buk2
EC: 2.7.2.7
UniProt
Find proteins for Q9X278 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X278 
Go to UniProtKB:  Q9X278
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X278
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
N [auth D],
O [auth D],
U [auth G],
V [auth G]
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
PO4
Query on PO4

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J [auth B],
Q [auth E],
R [auth E],
S [auth F],
W [auth H]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth A],
K [auth B],
L [auth C],
P [auth D],
T [auth F]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
M [auth D]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.261 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.68α = 90
b = 193.68β = 90
c = 122.932γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-30
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description