5HO9
Structure of truncated AbnA (domains 1-3), a GH43 arabinanase from Geobacilllus stearothermophilus, in complex with arabinooctaose
- PDB DOI: https://doi.org/10.2210/pdb5HO9/pdb
- Classification: HYDROLASE
- Organism(s): Geobacillus stearothermophilus
- Expression System: Escherichia coli
- Mutation(s): No 
- Deposited: 2016-01-19 Released: 2017-02-01 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.85 Å
- R-Value Free: 0.242 
- R-Value Work: 0.183 
- R-Value Observed: 0.185 
wwPDB Validation   3D Report Full Report
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Extracellular arabinanase | 639 | Geobacillus stearothermophilus | Mutation(s): 0  Gene Names: abnA | ||
UniProt | |||||
Find proteins for B3EYN2 (Geobacillus stearothermophilus) Explore B3EYN2  Go to UniProtKB:  B3EYN2 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | B3EYN2 | ||||
Sequence AnnotationsExpand | |||||
|
Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose | C, D | 8 | N/A | ||
Glycosylation Resources | |||||
GlyTouCan:  G91389JD GlyCosmos:  G91389JD |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PEG Query on PEG | CA [auth B] DA [auth B] EA [auth B] FA [auth B] GA [auth B] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N | |||
SO4 Query on SO4 | AA [auth B] BA [auth B] E [auth A] F [auth A] G [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.85 Å
- R-Value Free: 0.242 
- R-Value Work: 0.183 
- R-Value Observed: 0.185 
- Space Group: P 61 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 129.172 | α = 90 |
b = 129.172 | β = 90 |
c = 488.364 | γ = 120 |
Software Name | Purpose |
---|---|
PHENIX | refinement |
XDS | data reduction |
XDS | data scaling |
PHASER | phasing |
Entry History 
Deposition Data
- Released Date: 2017-02-01  Deposition Author(s): Lansky, S., Salama, R., Azoulai, D., Shwartstien, O., Shoham, Y., Shoham, G.
Revision History (Full details and data files)
- Version 1.0: 2017-02-01
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary