2GRJ | pdb_00002grj

Crystal structure of Dephospho-CoA kinase (EC 2.7.1.24) (Dephosphocoenzyme A kinase) (tm1387) from THERMOTOGA MARITIMA at 2.60 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.245 (Depositor), 0.239 (DCC) 
  • R-Value Work: 
    0.191 (Depositor) 
  • R-Value Observed: 
    0.193 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history. 

Literature

Crystal structure of Dephospho-CoA kinase (EC 2.7.1.24) (Dephosphocoenzyme A kinase) (tm1387) from THERMOTOGA MARITIMA at 2.60 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content 

  • Total Structure Weight: 185.56 kDa 
  • Atom Count: 11,485 
  • Modeled Residue Count: 1,432 
  • Deposited Residue Count: 1,536 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dephospho-CoA kinase
A, B, C, D, E
A, B, C, D, E, F, G, H
192Thermotoga maritimaMutation(s): 4 
Gene Names: coaE
EC: 2.7.1.24
UniProt
Find proteins for Q9X1A7 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9X1A7 
Go to UniProtKB:  Q9X1A7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9X1A7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
COD

Query on COD


Download:Ideal Coordinates CCD File
BA [auth H]
J [auth A]
L [auth B]
O [auth C]
Q [auth D]
BA [auth H],
J [auth A],
L [auth B],
O [auth C],
Q [auth D],
U [auth E],
W [auth F],
Y [auth G]
DEPHOSPHO COENZYME A
C21 H35 N7 O13 P2 S
KDTSHFARGAKYJN-IBOSZNHHSA-N
ADP

Query on ADP


Download:Ideal Coordinates CCD File
AA [auth H]
I [auth A]
K [auth B]
N [auth C]
P [auth D]
AA [auth H],
I [auth A],
K [auth B],
N [auth C],
P [auth D],
T [auth E],
V [auth F],
X [auth G]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
CL

Query on CL


Download:Ideal Coordinates CCD File
M [auth C],
R [auth E],
S [auth E],
Z [auth H]		CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.245 (Depositor), 0.239 (DCC) 
  • R-Value Work:  0.191 (Depositor) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.832α = 90
b = 87.217β = 106.92
c = 98.586γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.4: 2023-01-25
    Changes: Database references, Derived calculations
  • Version 1.5: 2024-11-20
    Changes: Data collection, Refinement description, Structure summary