3WH9

The ligand-free structure of ManBK from Aspergillus niger BK01

• PDB DOI: https://doi.org/10.2210/pdb3WH9/pdb

• Classification: HYDROLASE
• Organism(s): Aspergillus niger
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2013-08-22 Released: 2014-10-08 
• Deposition Author(s): Huang, J.W., Chen, C.C., Huang, C.H., Huang, T.Y., Wu, T.H., Cheng, Y.S., Ko, T.P., Lin, C.Y., Liu, J.R., Guo, R.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.190 
• R-Value Work: 0.159 

Starting Model: experimental

Literature

Structural Analysis and Rational Design to Improve Specific Activity of beta-Mannanase from Aspergillus Niger BK01

Huang, J.W., Chen, C.C., Huang, C.H., Huang, T.Y., Wu, T.H., Cheng, Y.S., Ko, T.P., Lin, C.Y., Liu, J.R., Guo, R.T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 76.95 kDa 
• Atom Count: 6,411 
• Modelled Residue Count: 690 
• Deposited Residue Count: 690 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endo-beta-1,4-mannanase	A, B	345	Aspergillus niger	Mutation(s): 0  EC: 3.2.1.78
UniProt
Find proteins for A2QKT4 (Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513)) Explore A2QKT4  Go to UniProtKB:  A2QKT4
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
TRS	F [auth A], I [auth B]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CL	G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 0.190 
• R-Value Work: 0.159 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.584	α = 90
b = 97.051	β = 90
c = 147.838	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-08 
Deposition Author(s): Huang, J.W., Chen, C.C., Huang, C.H., Huang, T.Y., Wu, T.H., Cheng, Y.S., Ko, T.P., Lin, C.Y., Liu, J.R., Guo, R.T.

Revision History  

• Version 1.0: 2014-10-08
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-30
  Changes: Structure summary