2C4M

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

PDB DOI: https://doi.org/10.2210/pdb2C4M/pdb

Classification: TRANSFERASE
Organism(s): Corynebacterium callunae
Expression System: Escherichia coli DH5[alpha]
Mutation(s): Yes

Deposited: 2005-10-20 Released: 2007-02-27
Deposition Author(s): Purvis, A., Nidetzky, B., Watson, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.232
R-Value Work: 0.216
R-Value Observed: 0.216

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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
Modelled Residue Count: 3,158
Deposited Residue Count: 3,184
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCOGEN PHOSPHORYLASE	A, B, C, D	796	Corynebacterium callunae	Mutation(s): 1 EC: 2.4.1.1
UniProt
Find proteins for Q8KQ56 (Corynebacterium callunae) Explore Q8KQ56 Go to UniProtKB: Q8KQ56
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8KQ56
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain HA [auth D] SDF format, chain P [auth B] SDF format, chain Y [auth C] MOL2 format, chain E [auth A] MOL2 format, chain HA [auth D] MOL2 format, chain P [auth B] MOL2 format, chain Y [auth C] mmCIF format, chain E [auth A] mmCIF format, chain HA [auth D] mmCIF format, chain P [auth B] mmCIF format, chain Y [auth C]	E [auth A], HA [auth D], P [auth B], Y [auth C]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain HA [auth D] Focus chain P [auth B] Focus chain Y [auth C]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain F [auth A] SDF format, chain IA [auth D] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain Z [auth C] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain F [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain Z [auth C] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain F [auth A] mmCIF format, chain IA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain Z [auth C]	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		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain F [auth A] Focus chain IA [auth D] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain Z [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain GA [auth C] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain GA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain GA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	GA [auth C], W [auth B], X [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain GA [auth C] Focus chain W [auth B] Focus chain X [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth C] SDF format, chain FA [auth C] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth D] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B]	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		Interactions Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain U [auth B] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.232
R-Value Work: 0.216
R-Value Observed: 0.216
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.266	α = 90
b = 187.62	β = 112.48
c = 129.315	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-02-27

Deposition Author(s):

Purvis, A.

Nidetzky, B.

Watson, K.

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