32XL | pdb_000032xl

Kineococcus siccus GH5_7 Mannanase, product bound

• PDB DOI: https://doi.org/10.2210/pdb32XL/pdb

• Classification: CARBOHYDRATE
• Organism(s): Kineococcus siccus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2026-07-29 Released: 2026-11-04 
• Deposition Author(s): Bloch, Y.
• Funding Organization(s): H2020 Marie Curie Actions of the European Commission

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free: 
  0.161 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.143 (DCC) 
• R-Value Observed: 
  0.143 (Depositor) 

Starting Model: in silico

Literature

Defining Glycosyl Hydrolase Family 5_7 mannan interaction through the identification and structural characterization of two Actinobacteria mannanases.

Bloch, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.49 kDa 
• Atom Count: 3,588 
• Modeled Residue Count: 371 
• Deposited Residue Count: 412 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GH5_7 Mannanase	A	412	Kineococcus siccus	Mutation(s): 0  EC: 3.2.1.78

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose	B	4		N/A

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose	C	3		N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MAN (Subject of Investigation/LOI)	D [auth A]	alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N
DMS (Subject of Investigation/LOI)	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.57 Å
• R-Value Free:  0.161 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.143 (DCC) 
• R-Value Observed: 0.143 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.97	α = 90
b = 75.57	β = 90
c = 99.25	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-11-04 
Deposition Author(s): Bloch, Y.

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Funding Organization	Location	Grant Number
H2020 Marie Curie Actions of the European Commission	European Union	945405

Revision History  

• Version 1.0: 2026-11-04
  Type: Initial release