1OCN | pdb_00001ocn

Mutant D416A of the CELLOBIOHYDROLASE CEL6A FROM HUMICOLA INSOLENS in complex with a cellobio-derived isofagomine at 1.3 angstrom resolution

PDB DOI: https://doi.org/10.2210/pdb1OCN/pdb

Classification: HYDROLASE
Organism(s): Mycothermus thermophilus
Expression System: Aspergillus oryzae
Mutation(s): No

Deposited: 2003-02-09 Released: 2003-05-22
Deposition Author(s): Varrot, A., Macdonald, J., Stick, R.V., Pell, G., Gilbert, H.J., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free:
0.162 (Depositor), 0.172 (DCC)
R-Value Work:
0.130 (Depositor), 0.147 (DCC)
R-Value Observed:
0.132 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Distortion of a Cellobio-Derived Isofagomine Highlights the Potential Conformational Itinerary of Inverting Beta-Glucosidases

Varrot, A., Macdonald, J., Stick, R.V., Pell, G., Gilbert, H.J., Davies, G.J.

(2003) Chem Commun (Camb) 21: 946

PubMed: 12744312 Search on PubMed
DOI: https://doi.org/10.1039/b301592k
Primary Citation Related Structures:
1OCN

PubMed Abstract:
A cellobio-derived isofagomine glycosidase inhibitor (Ki approximately 400 nM) displays an unusual distorted 2,5B (boat) conformation upon binding to cellobiohydrolase Cel6A from Humicola insolens, highlighting the different conformational itineraries used by various glycosidases, with consequences for the design of therapeutic agents.

Organizational Affiliation

Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, UK Y010 5YW.

Macromolecule Content

Total Structure Weight: 40.93 kDa
Atom Count: 3,407
Modeled Residue Count: 360
Deposited Residue Count: 362
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CELLOBIOHYDROLASE II	A	362	Mycothermus thermophilus	Mutation(s): 0 EC: 3.2.1.91
UniProt
Find proteins for Q9C1S9 (Humicola insolens) Explore Q9C1S9 Go to UniProtKB: Q9C1S9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9C1S9
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG 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]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
BGC Query on BGC Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A]	D [auth A], F [auth A]	beta-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-VFUOTHLCSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Interactions & Density Focus chain D [auth A] Focus chain F [auth A]
IFM Query on IFM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain C [auth A]	C [auth A], E [auth A]	5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE C₆ H₁₃ N O₃ QPYJXFZUIJOGNX-HSUXUTPPSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain E [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.31 Å
R-Value Free: 0.162 (Depositor), 0.172 (DCC)
R-Value Work: 0.130 (Depositor), 0.147 (DCC)
R-Value Observed: 0.132 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.357	α = 90
b = 69.842	β = 113.52
c = 51.95	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2003-05-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2003-05-22
Type: Initial release
Version 1.1: 2015-07-15
Changes: Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.3: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2024-10-23
Changes: Structure summary