4D3Y | pdb_00004d3y

The structure of inactive prolegumain from chinese hamster.

• PDB DOI: https://doi.org/10.2210/pdb4D3Y/pdb

• Classification: HYDROLASE
• Organism(s): Cricetulus griseus
• Mutation(s): No 


• Deposited: 2014-10-24 Released: 2016-01-20 
• Deposition Author(s): Li, W., Heinz, D.W., Krausze, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.241 (Depositor), 0.245 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.174 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

A Detailed Look Into Chinese Hamster Legumain Active Site Structure and Exploration of its Function

Li, W., Damme, M., Buessow, K., Grimm, I., Van Den Heuvel, J., Heinz, D.W., Krausze, J.

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)

Macromolecule Content 

• Total Structure Weight: 47.38 kDa 
• Atom Count: 3,187 
• Modeled Residue Count: 386 
• Deposited Residue Count: 408 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LEGUMAIN	A	408	Cricetulus griseus	Mutation(s): 0  EC: 3.4.22.34
UniProt
Find proteins for G3I1H5 (Cricetulus griseus) Explore G3I1H5  Go to UniProtKB:  G3I1H5
Glycosylation
Glycosylation Sites: 3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B [auth A], C [auth A], D [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
SNN	A	L-PEPTIDE LINKING	C4 H6 N2 O2		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.241 (Depositor), 0.245 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.174 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.27	α = 90
b = 60.33	β = 90
c = 153.95	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Li, W., Heinz, D.W., Krausze, J.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-12-20
  Changes: Refinement description