4WOU | pdb_00004wou

Crystal Structure of Mtb PEPCK in complex with GDP and metals

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.211 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.179 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 

Literature

Crystal Structure of Mtb PEPCK in complex with GDP and metals

Kim, H.L., Kriger, I.V., Sacchettini, J.C.

To be published.

Macromolecule Content 

  • Total Structure Weight: 69.8 kDa 
  • Atom Count: 5,018 
  • Modeled Residue Count: 595 
  • Deposited Residue Count: 622 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphoenolpyruvate carboxykinase [GTP]622Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: pckG, MRA_0219
EC: 4.1.1.32
UniProt
Find proteins for A5TYT6 (Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra))
Explore A5TYT6 
Go to UniProtKB:  A5TYT6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5TYT6
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP

Query on GDP


Download:Ideal Coordinates CCD File
B [auth A]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
PO4

Query on PO4


Download:Ideal Coordinates CCD File
F [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL


Download:Ideal Coordinates CCD File
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN

Query on ZN


Download:Ideal Coordinates CCD File
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MN

Query on MN


Download:Ideal Coordinates CCD File
D [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.211 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.179 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.316α = 90
b = 125.172β = 90
c = 122.147γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
d*TREKdata scaling

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: 2015-11-04
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Derived calculations, Refinement description
  • Version 1.2: 2023-12-27
    Changes: Data collection, Database references, Derived calculations