2C4M | pdb_00002c4m

Starch phosphorylase: structural studies explain oxyanion-dependent kinetic stability and regulatory control.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.232 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.216 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.216 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 2C4M

Ligand Structure Quality Assessment 


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

Literature

Starch Phosphorylase: Structural Studies Explain Oxyanion-Dependent Kinetic Stability and Regulatory Control

Purvis, A., Nidetzky, B., Watson, K.

To be published.

Macromolecule Content 

  • Total Structure Weight: 365.56 kDa 
  • Atom Count: 26,654 
  • Modeled Residue Count: 3,158 
  • Deposited Residue Count: 3,184 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLYCOGEN PHOSPHORYLASE
A, B, C, D
796Corynebacterium callunaeMutation(s): 1 
EC: 2.4.1.1
UniProt
Find proteins for Q8KQ56 (Corynebacterium callunae)
Explore Q8KQ56 
Go to UniProtKB:  Q8KQ56
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KQ56
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PLP

Query on PLP


Download:Ideal Coordinates CCD File
E [auth A],
HA [auth D],
P [auth B],
Y [auth C]		PYRIDOXAL-5'-PHOSPHATE
C8 H10 N O6 P
NGVDGCNFYWLIFO-UHFFFAOYSA-N
PO4

Query on PO4


Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
F [auth A]
IA [auth D]
Q [auth B]
AA [auth C],
BA [auth C],
F [auth A],
IA [auth D],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
Z [auth C]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO

Query on EDO


Download:Ideal Coordinates CCD File
GA [auth C],
W [auth B],
X [auth B]		1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT

Query on FMT


Download:Ideal Coordinates CCD File
CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
G [auth A]
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
JA [auth D],
K [auth A],
KA [auth D],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
O [auth A],
U [auth B],
V [auth B]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.232 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.216 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.216 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.266α = 90
b = 187.62β = 112.48
c = 129.315γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-27
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-28
    Changes: Advisory, Source and taxonomy
  • Version 1.4: 2019-05-08
    Changes: Data collection, Derived calculations, Experimental preparation
  • Version 1.5: 2023-12-13
    Changes: Advisory, Data collection, Database references, Other, Refinement description