1X9D

Crystal Structure Of Human Class I alpha-1,2-Mannosidase In Complex With Thio-Disaccharide Substrate Analogue

• PDB DOI: https://doi.org/10.2210/pdb1X9D/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2004-08-20 Released: 2005-02-22 
• Deposition Author(s): Karaveg, K., Tempel, W., Liu, Z.J., Siriwardena, A., Moremen, K.W., Wang, B.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.162 
• R-Value Work: 0.144 
• R-Value Observed: 0.146 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 62.03 kDa 
• Atom Count: 4,079 
• Modelled Residue Count: 452 
• Deposited Residue Count: 538 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase	A	538	Homo sapiens	Mutation(s): 0  Gene Names: MAN1B1 EC: 3.2.1.113
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UKM7 (Homo sapiens) Explore Q9UKM7  Go to UniProtKB:  Q9UKM7
PHAROS:  Q9UKM7 GTEx:  ENSG00000177239

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-methyl 2-thio-alpha-D-mannopyranoside	B	2	N/A	N/A
Glycosylation Resources
GlyTouCan:  G32183TR GlyCosmos:  G32183TR

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BU1	E [auth A]	1,4-BUTANEDIOL C4 H10 O2 WERYXYBDKMZEQL-UHFFFAOYSA-N
CA	C [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_900033	B	methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.162 
• R-Value Work: 0.144 
• R-Value Observed: 0.146 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.687	α = 89.49
b = 53.878	β = 63.6
c = 56.234	γ = 62.61

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-22 
Deposition Author(s): Karaveg, K., Tempel, W., Liu, Z.J., Siriwardena, A., Moremen, K.W., Wang, B.C.

Revision History  

• Version 1.0: 2005-02-22
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary