3A23

Crystal Structure of beta-L-Arabinopyranosidase complexed with D-galactose

PDB DOI: https://doi.org/10.2210/pdb3A23/pdb

Classification: HYDROLASE
Organism(s): Streptomyces avermitilis
Expression System: Streptomyces lividans
Mutation(s): No

Deposited: 2009-04-27 Released: 2009-07-14
Deposition Author(s): Fujimoto, Z., Ichinose, H., Kaneko, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.177
R-Value Work: 0.142
R-Value Observed: 0.144

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 132.13 kDa
Atom Count: 10,835
Modelled Residue Count: 1,226
Deposited Residue Count: 1,228
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative secreted alpha-galactosidase	A, B	614	Streptomyces avermitilis	Mutation(s): 0 Gene Names: agaA2, SAV2186, SAV_2186
UniProt
Find proteins for Q82L26 (Streptomyces avermitilis (strain ATCC 31267 / DSM 46492 / JCM 5070 / NBRC 14893 / NCIMB 12804 / NRRL 8165 / MA-4680)) Explore Q82L26 Go to UniProtKB: Q82L26
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q82L26
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1PG Query on 1PG Download Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain P [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain P [auth A]	DA [auth B], P [auth A]	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C₁₁ H₂₄ O₆ SLNYBUIEAMRFSZ-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain P [auth A] Interactions & Density Focus chain DA [auth B] Focus chain P [auth A]
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain CA [auth B] MOL2 format, chain CA [auth B]	CA [auth B]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Interactions & Density Focus chain CA [auth B]
GAL Query on GAL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain C [auth A] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B]	C [auth A], T [auth B], U [auth B]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain C [auth A] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain C [auth A] Focus chain T [auth B] Focus chain U [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A]	EA [auth B], FA [auth B], Q [auth A], R [auth A], S [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain EA [auth B] Focus chain FA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain EA [auth B] Focus chain FA [auth B] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain O [auth A] SDF format, chain V [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain O [auth A] MOL2 format, chain V [auth B]	AA [auth B] BA [auth B] D [auth A] E [auth A] F [auth A] AA [auth B], BA [auth B], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
GAL	Binding MOAD: 3A23	Ka: 610 (M^-1) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.177
R-Value Work: 0.142
R-Value Observed: 0.144
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.256	α = 90
b = 99.081	β = 90
c = 181.63	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-07-14

Deposition Author(s):

Fujimoto, Z.

Ichinose, H.

Kaneko, S.

Revision History (Full details and data files)

Version 1.0: 2009-07-14
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-11-01
Changes: Data collection, Database references, Refinement description, Structure summary