1P4J | pdb_00001p4j

Crystal structure of glycogen phosphorylase b in complex with C-(1-hydroxy-beta-D-glucopyranosyl)formamide

PDB DOI: https://doi.org/10.2210/pdb1P4J/pdb

Classification: TRANSFERASE
Organism(s): Oryctolagus cuniculus
Mutation(s): No

Deposited: 2003-04-23 Released: 2004-05-18
Deposition Author(s): Chrysina, E.D., Oikonomakos, N.G., Zographos, S.E., Kosmopoulou, M.N., Bischler, N., Leonidas, D.D., Nagy, V., Somsak, L., Gergely, P., Praly, J.-P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.198 (Depositor)
R-Value Work:
0.181 (Depositor)
R-Value Observed:
0.181 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crsytallographic Studies on alpha- and beta-D-glucopyranosyl Formamide Analogues, Inhibitors of Glycogen Phosphorylase

Chrysina, E.D., Oikonomakos, N.G., Zographos, S.E., Kosmopoulou, M.N., Bischler, N., Leonidas, D.D., Kovacs, L., Docsa, T., Gergely, P., Somsak, L.

(2003) Biocatal Biotransformation 21: 233-242

DOI: https://doi.org/10.1080/10242420310001614360

Macromolecule Content

Total Structure Weight: 97.76 kDa
Atom Count: 6,982
Modeled Residue Count: 810
Deposited Residue Count: 842
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycogen phosphorylase, muscle form	A	842	Oryctolagus cuniculus	Mutation(s): 0 EC: 2.4.1.1
UniProt
Find proteins for P00489 (Oryctolagus cuniculus) Explore P00489 Go to UniProtKB: P00489
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00489
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain B [auth A]
CBF Query on CBF Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(2R,3R,4S,5S,6R)-2,3,4,5-tetrahydroxy-6-(hydroxymethyl)oxane-2-carboxamide C₇ H₁₃ N O₇ DTZYCNDAJQDPQC-UHKLXPPTSA-N		Interactions Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.198 (Depositor)
R-Value Work: 0.181 (Depositor)
R-Value Observed: 0.181 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.16	α = 90
b = 128.16	β = 90
c = 116.01	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MAR345	data collection
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2004-05-18

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-05-18
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-11
Changes: Refinement description
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.5: 2023-10-25
Changes: Data collection, Database references, Refinement description, Structure summary