3QFY | pdb_00003qfy

Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase Complexed with Sulfate and Isofagomine

PDB DOI: https://doi.org/10.2210/pdb3QFY/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Cellulomonas gilvus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-01-24 Released: 2011-09-21
Deposition Author(s): Fushinobu, S., Hidaka, M., Hayashi, A.M., Wakagi, T., Shoun, H., Kitaoka, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.208 (Depositor), 0.211 (DCC)
R-Value Work:
0.138 (Depositor), 0.141 (DCC)
R-Value Observed:
0.141 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Interactions between glycoside hydrolase family 94 cellobiose phosphorylase and glucosidase inhibitors

Fushinobu, S., Hidaka, M., Hayashi, A.M., Wakagi, T., Shoun, H., Kitaoka, M.

(2011) J Appl Glycosci (1999) 58: 91-97

DOI: https://doi.org/10.5458/jag.jag.JAG-2010_022

Macromolecule Content

Total Structure Weight: 187.52 kDa
Atom Count: 14,083
Modeled Residue Count: 1,644
Deposited Residue Count: 1,684
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cellobiose Phosphorylase	A, B	842	Cellulomonas gilvus	Mutation(s): 0 EC: 2.4.1.20
UniProt
Find proteins for O66264 (Cellulomonas gilvus) Explore O66264 Go to UniProtKB: O66264
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O66264
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
IFM Query on IFM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B]	E [auth A], K [auth B]	5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE C₆ H₁₃ N O₃ QPYJXFZUIJOGNX-HSUXUTPPSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain J [auth B] MOL2 format, chain D [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain J [auth B] mmCIF format, chain D [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain J [auth B]	D [auth A], G [auth A], H [auth A], J [auth B], L [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth B] Interactions & Density Focus chain D [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.208 (Depositor), 0.211 (DCC)
R-Value Work: 0.138 (Depositor), 0.141 (DCC)
R-Value Observed: 0.141 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.71	α = 90
b = 98.254	β = 102.73
c = 104.45	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2011-09-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-09-21
Type: Initial release
Version 1.1: 2015-08-12
Changes: Non-polymer description
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary
Version 1.4: 2024-03-20
Changes: Data collection, Database references, Structure summary

3QFY | pdb_00003qfy

Crystal Structure of Cellvibrio gilvus Cellobiose Phosphorylase Complexed with Sulfate and Isofagomine

Literature

Interactions between glycoside hydrolase family 94 cellobiose phosphorylase and glucosidase inhibitors

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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