5YNC
Crystal structure of Pullulanase from Klebsiella pneumoniae complex at 1 mM beta-cyclodextrin
- PDB DOI: https://doi.org/10.2210/pdb5YNC/pdb
- Classification: HYDROLASE
- Organism(s): Klebsiella pneumoniae
- Mutation(s): No 
- Deposited: 2017-10-24 Released: 2018-10-24 
- Funding Organization(s): Japan Society for the Promotion of Science
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.32 Å
- R-Value Free: 0.254 
- R-Value Work: 0.187 
- R-Value Observed: 0.191 
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 |
PulA protein | 1,102 | Klebsiella pneumoniae | Mutation(s): 0  | ||
UniProt | |||||
Find proteins for W9BQ28 (Klebsiella pneumoniae) Explore W9BQ28  Go to UniProtKB:  W9BQ28 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | W9BQ28 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 3 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GOL Query on GOL | K [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
ACT Query on ACT | I [auth A], J [auth A] | ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M | |||
CA Query on CA | D [auth A], E [auth A], F [auth A], G [auth A], H [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_900012 Query on PRD_900012 | B, C | beta-cyclodextrin | Oligosaccharide / Drug delivery |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.32 Å
- R-Value Free: 0.254 
- R-Value Work: 0.187 
- R-Value Observed: 0.191 
- Space Group: P 43 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 88.925 | α = 90 |
b = 88.925 | β = 90 |
c = 299.527 | γ = 90 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
MOLREP | phasing |
PHENIX | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
Entry History & Funding Information
Deposition Data
- Released Date: 2018-10-24  Deposition Author(s): Saka, N., Iwamoto, H., Takahashi, N., Mizutani, K., Mikami, B.
Funding Organization | Location | Grant Number |
---|---|---|
Japan Society for the Promotion of Science | Japan | 16H04909 |
Revision History (Full details and data files)
- Version 1.0: 2018-10-24
Type: Initial release - Version 1.1: 2018-11-14
Changes: Data collection, Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-11-22
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary