4G1P | pdb_00004g1p

Structural and Mechanistic Basis of Substrate Recognition by Novel Di-peptidase Dug1p From Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb4G1P/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-07-11 Released: 2013-07-17 
• Deposition Author(s): Singh, A.K., Singh, M., Pandya, V.K., Singh, V., Mittal, M., Kumaran, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.231 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structural and Mechanistic Basis of Substrate Recognition by Novel Di-peptidase Dug1p From Saccromyces cerevesiae

Singh, A.K., Singh, M., Pandya, V.K., Singh, V., Mittal, M., Kumaran, S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 54.09 kDa 
• Atom Count: 3,882 
• Modeled Residue Count: 479 
• Deposited Residue Count: 487 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cys-Gly metallodipeptidase DUG1	A	487	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: Dug1p EC: 3.4.13
UniProt
Find proteins for P43616 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P43616  Go to UniProtKB:  P43616

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CYS	E [auth A]	CYSTEINE C3 H7 N O2 S XUJNEKJLAYXESH-REOHCLBHSA-N
GLY	D [auth A]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.231 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.132	α = 90
b = 119.132	β = 90
c = 176.302	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASES	phasing
PHENIX	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-17 
Deposition Author(s): Singh, A.K., Singh, M., Pandya, V.K., Singh, V., Mittal, M., Kumaran, S.

Revision History  

• Version 1.0: 2013-07-17
  Type: Initial release
  
• Version 1.1: 2014-09-17
  Changes: Other
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description