1UZ4 | pdb_00001uz4

Common inhibition of beta-glucosidase and beta-mannosidase by isofagomine lactam reflects different conformational intineraries for glucoside and mannoside hydrolysis

PDB DOI: https://doi.org/10.2210/pdb1UZ4/pdb

Classification: HYDROLASE
Organism(s): Cellvibrio mixtus
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2004-03-04 Released: 2004-11-03
Deposition Author(s): Vincent, F., Davies, G.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free:
0.165 (Depositor), 0.180 (DCC)
R-Value Work:
0.133 (Depositor), 0.150 (DCC)
R-Value Observed:
0.135 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Common Inhibition of Both Beta-Glucosidases and Beta-Mannosidases by Isofagomine Lactam Reflects Different Conformational Itineraries for Pyranoside Hydrolysis

Vincent, F., Gloster, T.M., Macdonald, J., Morland, C., Stick, R.V., Dias, F., Prates, J., Fontes, C.M.G.A., Gilbert, H.J., Davies, G.J.

(2004) Chembiochem 5: 1596

PubMed: 15515081 Search on PubMed
DOI: https://doi.org/10.1002/cbic.200400169
Primary Citation of Related Structures:
1UZ1, 1UZ4

Organizational Affiliation

Structural Biology Laboratory, Department of Chemistry, The University of York, Heslington, York, YO10 5YW, UK.

Macromolecule Content

Total Structure Weight: 50.76 kDa
Atom Count: 3,870
Modeled Residue Count: 410
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAN5A	A	440	Cellvibrio mixtus	Mutation(s): 0
UniProt
Find proteins for Q6QT42 (Cellvibrio mixtus) Explore Q6QT42 Go to UniProtKB: Q6QT42
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6QT42
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IFL Query on IFL 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]	(3S,4R,5R)-3,4-DIHYDROXY-5-(HYDROXYMETHYL)PIPERIDIN-2-ONE C₆ H₁₁ N O₄ ARBXEMIAJIJEQI-WDCZJNDASA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	C [auth A], D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.71 Å
R-Value Free: 0.165 (Depositor), 0.180 (DCC)
R-Value Work: 0.133 (Depositor), 0.150 (DCC)
R-Value Observed: 0.135 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.625	α = 90
b = 102.37	β = 90
c = 50.356	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

Entry History

Deposition Data

Released Date: 2004-11-03

Deposition Author(s):

Vincent, F.

Davies, G.J.

Revision History (Full details and data files)

Version 1.0: 2004-11-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2023-12-13
Changes: Data collection, Database references, Other, Refinement description

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Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 1UZ4 | pdb_00001uz4

Common inhibition of beta-glucosidase and beta-mannosidase by isofagomine lactam reflects different conformational intineraries for glucoside and mannoside hydrolysis

Common Inhibition of Both Beta-Glucosidases and Beta-Mannosidases by Isofagomine Lactam Reflects Different Conformational Itineraries for Pyranoside Hydrolysis

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations