2YDP | pdb_00002ydp

Structure of the E242A mutant of the alpha-l-arabinofuranosidase arb93a from fusarium graminearum in complex with an iminosugar inhibitor

PDB DOI: https://doi.org/10.2210/pdb2YDP/pdb

Classification: HYDROLASE
Organism(s): Fusarium graminearum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2011-03-24 Released: 2011-07-13
Deposition Author(s): Goddard-Borger, E.D., Carapito, R., Jeltsch, J.M., Phalip, V., Stick, R.V., Varrot, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.226 (Depositor), 0.230 (DCC)
R-Value Work:
0.171 (Depositor), 0.170 (DCC)
R-Value Observed:
0.174 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Alpha-L-Arabinofuranosylated Pyrrolidines as Arabinanase Inhibitors.

Goddard-Borger, E.D., Carapito, R., Jeltsch, J., Phalip, V., Stick, R.V., Varrot, A.

(2011) Chem Commun (Camb) 47: 9684

PubMed: 21773614 Search on PubMed
DOI: https://doi.org/10.1039/c1cc13675e
Primary Citation of Related Structures:
2YDP, 2YDT

PubMed Abstract:
As part of continued efforts to understand the mechanisms of 1,5-α-l-arabinanases better, some arabinan-like iminosugar oligosaccharides were synthesized. An iminosugar analogue of arabinobiose was found to be a good inhibitor of the arabinanase Arb93A from Fusarium graminearum. Structures were determined for complexes of this inhibitor with wild-type Arb93A and a catalytically inactive mutant.

Organizational Affiliation

School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.

Macromolecule Content

Total Structure Weight: 124.16 kDa
Atom Count: 9,600
Modeled Residue Count: 1,079
Deposited Residue Count: 1,101
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXO-1,5-ALPHA-L-ARABINOFURANOBIOSIDASE	A, B, C	367	Fusarium graminearum	Mutation(s): 1 EC: 3.2.1.55
UniProt
Find proteins for B8ZY56 (Gibberella zeae) Explore B8ZY56 Go to UniProtKB: B8ZY56
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8ZY56
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AHR Query on AHR Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] SDF format, chain K [auth C] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C]	E [auth A], H [auth B], K [auth C]	alpha-L-arabinofuranose C₅ H₁₀ O₅ HMFHBZSHGGEWLO-QMKXCQHVSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain K [auth C]
EDG Query on EDG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain G [auth B] SDF format, chain J [auth C] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain J [auth C] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain J [auth C]	D [auth A], G [auth B], J [auth C]	1,4-DIDEOXY-1,4-IMINO-L-ARABINITOL C₅ H₁₁ N O₃ OQEBIHBLFRADNM-YUPRTTJUSA-N		Interactions Focus chain D [auth A] Focus chain G [auth B] Focus chain J [auth C] Interactions & Density Focus chain D [auth A] Focus chain G [auth B] Focus chain J [auth C]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C]	F [auth A], I [auth B], L [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.226 (Depositor), 0.230 (DCC)
R-Value Work: 0.171 (Depositor), 0.170 (DCC)
R-Value Observed: 0.174 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.93	α = 90.14
b = 57.8	β = 93.55
c = 91.6	γ = 114.5

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-07-13

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-07-13
Type: Initial release
Version 1.1: 2011-11-16
Changes: Database references, Refinement description, Version format compliance
Version 1.2: 2015-04-01
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary