5JAW | pdb_00005jaw

Structure of a beta galactosidase with inhibitor

PDB DOI: https://doi.org/10.2210/pdb5JAW/pdb

Classification: HYDROLASE
Organism(s): Cellvibrio japonicus Ueda107
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-04-12 Released: 2017-05-10
Deposition Author(s): Offen, W., Davies, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.214 (Depositor), 0.219 (DCC)
R-Value Work:
0.197 (Depositor)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Towards broad spectrum activity-based glycosidase probes: synthesis and evaluation of deoxygenated cyclophellitol aziridines.

Schroder, S.P., van de Sande, J.W., Kallemeijn, W.W., Kuo, C.L., Artola, M., van Rooden, E.J., Jiang, J., Beenakker, T.J.M., Florea, B.I., Offen, W.A., Davies, G.J., Minnaard, A.J., Aerts, J.M.F.G., Codee, J.D.C., van der Marel, G.A., Overkleeft, H.S.

(2017) Chem Commun (Camb) 53: 12528-12531

PubMed: 29116266 Search on PubMed
DOI: https://doi.org/10.1039/c7cc07730k
Primary Citation Related Structures:
5JAW

PubMed Abstract:
Activity-based protein profiling has emerged as a powerful tool for visualizing glycosidases in complex biological samples. Several configurational cyclophellitol isomers have been shown to display high selectivity as probes for glycosidases processing substrates featuring the same configuration. Here, a set of deoxygenated cyclophellitols are presented which enable inter-class profiling of β-glucosidases and β-galactosidases.

Organizational Affiliation

Department of Bioorganic Synthesis, Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands. h.s.overkleeft@chem.leidenuniv.nl.

Macromolecule Content

Total Structure Weight: 499.2 kDa
Atom Count: 35,244
Modeled Residue Count: 4,249
Deposited Residue Count: 4,400
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-galactosidase, putative, bgl35A	A, B, C, D, E A, B, C, D, E, F, G, H	550	Cellvibrio japonicus Ueda107	Mutation(s): 0 Gene Names: bgl35A, CJA_2707 EC: 3.2.1.23
UniProt
Find proteins for B3PBE0 (Cellvibrio japonicus (strain Ueda107)) Explore B3PBE0 Go to UniProtKB: B3PBE0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B3PBE0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UUU Query on UUU Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain V [auth D] SDF format, chain Q [auth C] SDF format, chain NA [auth H] SDF format, chain M [auth B] SDF format, chain JA [auth G] SDF format, chain I [auth A] SDF format, chain GA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain V [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain NA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain JA [auth G] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain V [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain NA [auth H] mmCIF format, chain M [auth B] mmCIF format, chain JA [auth G] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth F]	GA [auth F] I [auth A] JA [auth G] M [auth B] NA [auth H] GA [auth F], I [auth A], JA [auth G], M [auth B], NA [auth H], Q [auth C], V [auth D], Z [auth E]	(1S,2S,3S,4S,5R,6R)-5-amino-6-(hydroxymethyl)cyclohexane-1,2,3,4-tetrol C₇ H₁₅ N O₅ SWVTZDDSAFUTKS-OUIVRQFQSA-N		Interactions Focus chain GA [auth F] Focus chain I [auth A] Focus chain JA [auth G] Focus chain M [auth B] Focus chain NA [auth H] Focus chain Q [auth C] Focus chain V [auth D] Focus chain Z [auth E] Interactions & Density Focus chain GA [auth F] Focus chain I [auth A] Focus chain JA [auth G] Focus chain M [auth B] Focus chain NA [auth H] Focus chain Q [auth C] Focus chain V [auth D] Focus chain Z [auth E]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain FA [auth E] MOL2 format, chain FA [auth E] mmCIF format, chain FA [auth E]	FA [auth E]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain FA [auth E] Interactions & Density Focus chain FA [auth E]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain PA [auth H] SDF format, chain P [auth B] SDF format, chain OA [auth H] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain MA [auth G] SDF format, chain LA [auth G] SDF format, chain L [auth A] SDF format, chain KA [auth G] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth F] SDF format, chain HA [auth F] SDF format, chain EA [auth E] SDF format, chain DA [auth E] SDF format, chain CA [auth E] SDF format, chain BA [auth E] SDF format, chain AA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain PA [auth H] MOL2 format, chain P [auth B] MOL2 format, chain OA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain MA [auth G] MOL2 format, chain LA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth G] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain HA [auth F] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] MOL2 format, chain AA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain PA [auth H] mmCIF format, chain P [auth B] mmCIF format, chain OA [auth H] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain MA [auth G] mmCIF format, chain LA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth G] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth F] mmCIF format, chain HA [auth F] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E] mmCIF format, chain AA [auth E]	AA [auth E] BA [auth E] CA [auth E] DA [auth E] EA [auth E] AA [auth E], BA [auth E], CA [auth E], DA [auth E], EA [auth E], HA [auth F], IA [auth F], J [auth A], K [auth A], KA [auth G], L [auth A], LA [auth G], MA [auth G], N [auth B], O [auth B], OA [auth H], P [auth B], PA [auth H], R [auth C], S [auth C], T [auth C], U [auth C], W [auth D], X [auth D], Y [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth G] Focus chain L [auth A] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain N [auth B] Focus chain O [auth B] Focus chain OA [auth H] Focus chain P [auth B] Focus chain PA [auth H] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain J [auth A] Focus chain K [auth A] Focus chain KA [auth G] Focus chain L [auth A] Focus chain LA [auth G] Focus chain MA [auth G] Focus chain N [auth B] Focus chain O [auth B] Focus chain OA [auth H] Focus chain P [auth B] Focus chain PA [auth H] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.214 (Depositor), 0.219 (DCC)
R-Value Work: 0.197 (Depositor)
R-Value Observed: 0.198 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.168	α = 90.15
b = 115.66	β = 90.11
c = 115.935	γ = 90.11

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2017-05-10

Deposition Author(s):

Offen, W.

Davies, G.

Funding Organization	Location	Grant Number
	United Kingdom	--

Revision History (Full details and data files)

Version 1.0: 2017-05-10
Type: Initial release
Version 1.1: 2018-01-10
Changes: Database references
Version 1.2: 2020-03-11
Changes: Derived calculations, Refinement description
Version 1.3: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2024-10-23
Changes: Structure summary